Accounts of the roots of Los Penitentes date back at least a thousand years to the flagellant orders in Spain and Italy. However, the current incarnation of the Brotherhood dates to the early 19th century. Following Mexican independence from Spain in 1821, Church authorities in Mexico withdrew the Franciscan, Dominican and Jesuit missionaries from its provinces, replacing them with secular priests. They failed, however, to replace the missionaries with an equal number of priests, depriving many secluded communities of a resident clergyman. Accordingly, many of those small communities could expect only a once-yearly visit from a parish priest.
The men in those communities eventually came together in the absence of a priest for the purpose of prayer, and to offer spiritual and social aid to the community. They gathered in meeting houses known as moradas. Los Penitentes were perhaps best known for their songs of worship, called alabados, and for their ascetic practices, which included self-flagellation in private ceremonies during Lent, and processions during Holy Week which ended with the reenactment of Christ’s crucifixion on Good Friday.
Archbishop Jean Baptiste Lamy and his successor, Jean Baptiste Salpointe, unsuccessfully attempted to suppress the brotherhood in the latter part of the 19th century as a part of the "Americanization" of the Church in New Mexico, driving its membership underground. For this reason, Los Penitentes are sometimes described as a “secret society”. The Brotherhood reconciled with the Church in the mid 20th century, receiving formal recognition in 1947, and Los Penitentes remain active in Northern New Mexico and southern Colorado to this day, although a depopulation of these regions after World War II has led to a decline in Penitente membership.