This cemetery is located on Madeline Island, off the coast of Bayfield Wisconsin, in Lake Superior. Madeline is part of the Apostle Islands group. The town of LaPointe (on Madeline Island), is an ancient settlement.

Being a well known historical site, this is one of the most visited historical cemeteries in the state of Wisconsin.

It was here in 1835 that Fr. Frederic Baraga built a Catholic mission. Three years later, Baraga built his second Catholic church on the Island (in a different location), which is where the present-day Catholic church is now located (St. Joseph Catholic Church, adjacent to Saint Joseph Cemetery).

This cemetery is generally considered to have been established in about 1836, about a year after the first Catholic Mission was built. It is probable that the cemetery includes older graves, as later archaeological studies have revealed several earlier ancient graves nearby. Many of the early tombstones still exist, but some are not readable anymore. Many graves are marked by wooden crosses, decorative fences, and/or traditional headstones.

This is the final resting place of many notable historical figures, including Great Buffalo, who was the principal chief of the Ojibwe people, and Madeline Cadotte, whom the island is named after.

The common name for this cemetery is misleading. Despite being called the "Indian Cemetery", many of the Island's original white settlers are buried here, among many Native Americans who were members of Father Baraga's first Catholic Mission. People buried here represent many different cultural/ethnic groups, such as Ojibwe, French-Canadian, and European.

Around the 1950s, the name "Indian Cemetery" was used in Madeline Island tourist literature, as a way to promote the cemetery as a historical tourist site. Subsequently, the name has stuck. But despite being commonly referred to as the "Indian Cemetery", in reality, this is the burial place of people with varied ethnic origin, who were associated with the Catholic church.

The small wooden structures over some of the Native American graves are known as Spirit Houses. These Spirit Houses are a centuries-old Ojibwe custom, and were built to protect the deceased in their journey to the afterlife.

Vandalism and the elements have taken their toll on this cemetery. While visiting the cemetery is encouraged, visitors are politely asked to view the cemetery from the edge of the metal gate, where there is an interpretive sign displaying the history of the site. Entry inside of the cemetery gate is no longer encouraged, with the exception of a family descendant needing access to a relative's plot. Please be respectful of this, when visiting.

In 1972, the Catholic Church transferred the ownership of the cemetery to the U.S. Government, allowing for federal money to be used for creating a breakwater, to end an ongoing issue the cemetery was having with lakeside erosion. And in 1977, the cemetery became listed on the National Register of Historic Places.

While the cemetery has long been honored for it's historical and cultural significance, it hasn't been without controversies. When the boat marina was being built directly next to the cemetery, it was claimed by some that part of the cemetery was disturbed, and some unmarked graves on the edge of the cemetery were unearthed, to make way for the new Marina development.

In the 1960s, many visitors and local people were disappointed by the lack of care and preservation for the cemetery, which caused it to look overgrown and abandoned. Some visitors dropped litter in the cemetery. Thankfully things have improved somewhat nowadays, with landscaping and upkeep improving.

The history and significance of the cemetery is discussed in the book, "Badger Boneyards", by author Dennis McCann, on pages 135-139. (ISBN 978-0-87020-451-7)

The cemetery is the subject of many legends, many involving the spirits of people buried there.

Identifying the location of some graves can be difficult, because many tombstones are missing or damaged. The actual number of burials here is unknown. According to administrators of Holy Family Catholic Church in Bayfield (where records are kept for the Catholic community on Madeline Island), the burial plat for this cemetery was lost many decades ago. However in 2014, some antique documents surfaced in a private collection, which were rumored to be the original burial records and plat for this cemetery. However, the information or documents haven't been released.