As early as 1906, federal legislation was passed to protect our cultural heritage. The National Historic Preservation Act of 1966 requires that agencies using federal funds consider archaeological sites in project development.

Wisconsin demonstrated its leadership in 1990 by strengthening state laws to include the protection of cemeteries and other burial areas. The Society is committed to protecting Wisconsin's heritage and works closely with the Wisconsin Department of Transportation (WisDOT) and the Federal Highway Administration to identify and protect significant sites. When designing roadways for the traveling public, WisDOT engineers make every effort to avoid archaeological sites and preserve Wisconsin's cultural diversity.

The Museum Archaeology Program began in response to the passage of the Federal-Aid Highway Act of 1956, popularly referred to as the Highway Salvage Act. Through this act, the government initiated the interstate highway program, a colossal, fifteen-year, $50 billion undertaking. The act included provisions for the protection and recovery of historic, archaeological, and paleontological resources. The act, however, did not make state compliance with these provisions mandatory. But Wisconsin's Highway Department created a procedure to allow limited archaeological research before highway construction.

The Highway Salvage Act also required each state to select an institutional sponsor for archaeology, although it did not include financial help for analysis and curation of archaeological collections. The Wisconsin Historical Society (Society) was one of only a few institutions which had personnel and funds to divert from its budget to meet the costs of conducting archaeological field research.

In 1958, Warren Wittry, then the Society's Curator of Anthropology, negotiated the first cooperative agreement between the Society and the State Highway Commission. This cooperative agreement stipulated that the Department of Transportation would provide money for field survey and excavation and that the Society would provide resources for transportation, analysis, report preparation, and curation. In that first year, two archaeologists surveyed 211 miles of highway right-of-way, discovering twenty-eight Native American sites, and two Euro-American cemeteries.

In 1960, Joan Freeman joined the Wisconsin Historical Society as the Curator of Anthropology, and hired its first sizable field crew. She was the first woman to receive a Ph.D. in Anthropology in Wisconsin, specializing in archaeology; and was also the first State Archaeologist. Joan Freeman also made an important contribution by supporting women in archaeology. hiring them for field positions. She encouraged and inspired many women who received advanced degrees in Anthropology, and who today are professional Archaeologists.

The Society did more archaeological excavation in Wisconsin during the next ten years (1960-1970), than had ever been done before by any university or institution. Freeman negotiated with the Department of Natural Resources for research support at Wisconsin's most famous archaeological site, Aztalan. Aztalan is located along on the west bank of the Crawfish River east of Lake Mills in Jefferson County. Society Archaeologists from the Museum worked at Aztalan for three years focusing on the stockade, the pyramidal mound, and the village area.

Archaeologists also worked at a state highway project at the Millville Site in Grant County, and discovered fourteen circular houses which formed a community or village plan. These Native American houses, approximately 1,600 years old, were the third such structures ever discovered in Wisconsin. Excavation costs were nominal. In 1964, when Freeman directed excavations at the Miller Site on Highway 60 in Crawford County, she and her crew of seven archaeologists had a budget of only $4,000 per month for salaries, food, and housing. The crew lived in a local farmhouse, and a cook was hired to prepare the meals.

The most important federal legislation affecting public archaeology was the National Historic Preservation Act of 1966. This legislation created the Section 106 compliance process, and established the National Register of Historic Places, the Advisory Council on Historic Preservation, and the state historic preservation offices and state review boards. In 1971 President Nixon changed the direction and momentum of public archaeology when he directed federal agencies, under Executive Order 11593, to take the lead role in preserving, restoring, and maintaining the nation's historic and cultural resources.

The Museum Archaeology Program branched out during this period, conducting field research for several federal agencies over the next ten years. In 1971, funded by the Army Corps of Engineers, the program began the first large-scale archaeological survey ever conducted in the state, the La Farge Reservoir Project. This was a ten-year study to locate archaeological sites in the Kickapoo River Valley in Vernon County, which was to have been dammed and flooded. The La Farge survey identified over 200 archaeological sites, providing the first complete sequence of more than 10,000 years of human occupation in Wisconsin.

Between 1975 and 1990 the number of public archaeology projects grew from fewer than twenty-five to over 600 each year. The Great River Road archaeological survey, conducted in only four years between 1979 and 1982, covered 152 miles through seven counties. A total of 242 new sites were discovered and 53 known sites were revisited. The Program was managed by one part-time position and also hired field archaeologists for the summer months.

In the late 1970's, John Penman, then Director of "Highway Archaeology" (today the Museum Archaeology Program), re-negotiated the program's cooperative agreement with the newly named Wisconsin Department of Transportation. The Department of Transportation agreed to pay for the entire cost of archaeological research, including analysis and report preparation. The Program was permitted to add 2 and 1/2 new positions, bringing the total Program staff to three full-time positions.

The State’s omnibus 1987 Historic Preservation legislation provided greater support for archaeological research, and the protection of archaeological sites. It also placed greater responsibility on state agencies to consider the effects of their construction projects and land management practices. The largest project ever conducted by Society Archaeologists, the La Crosse Freeway Project, began in 1985. Over a nine year period, more than 200 archaeologists have worked on it both in the field and in the laboratory.

The most significant discovery, what is now known as the Tremaine Site, was made just north of La Crosse near Holmen. There archaeologists identified a community from the Oneota culture of seven long houses, each over forty meters (130 feet) long and approximately 500 years old. While many Oneota sites had been studied in the La Crosse locality, no structures had ever before been recognized.

Laboratory analysis for the project has contributed significantly to understanding of Oneota culture. Wood charcoal analysis indicates how the Oneota depleted local forest resources, clearing them for planting and using available wood for cooking, heating, and construction. A series of more than thirty radiocarbon dates for this site has suggested how long the Oneota occupied the site and the sequence of construction.

In response to the growing need for ethnobotanical analysis (how ethnic groups use plants), the program established a paleoethnobotany lab in 1992, and in 1993 entered into a cooperative agreement with the anthropology department at UW-Madison to curate its ethnobotanical collection and to exchange newly acquired specimens. In 1998 the Program added a Faunal Analyst to the staff, making subsistence research a Program focus.

That same year MAP began offering professional architectural history services to assist agencies in the identification of historic buildings and structures which may be affected by development and construction projects.

The Museum Archaeology Program is the active research branch of the Society. Staffing has increased from one half-time position in 1960, to nine full-time positions today. The Program operates with a year-round staff of twenty, and a seasonal staff of between thirty to fifty archaeologists. During its 56-year history, over 1,250 student and professional archaeologists and architectural historians have participated in the completion of nearly 5,000 field projects. The Program continues to train students, interns and volunteers in archaeological field methods and techniques, laboratory methods and techniques, and in the curation of archaeological collections.

The MAP continues to support, advance and encourage archaeological research in Wisconsin. Many questions remain to be asked to understand Wisconsin’s rich cultural history. Archaeology provides critical pieces to the puzzle of human history through its ability to study peoples who did not write their story down.