Unfortunately, there's not a lot of information available on the Ais and Jaega, so I'll be focusing on the Calusa. They were the dominant power in southern Florida until the 1700s, and their influence extended over the Jaega and possibly the Ais as well (it's a bit unclear whether the Ais were actually subordinate to the Calusa or whether they were just closely allied).

At the top of the Calusa pantheon were three gods. The highest of these governed the motion of the heavens and the turn of seasons. The second oversaw the fate of nations. The third dictated the course of battles. There may be lesser spirits as well. For example, the Spanish reported a "god of the cemetery," who was represented with a carving of a bird (probably something similar to the Fort Center Eagle), though whether this presented an actual spirit or if the Spanish were just eager to cry idolatry whenever they could is unknown.

For the Calusa, the human soul was composed of three parts. One resided in a person's shadow, one in a person's reflection, and one in a person's eyes. Only this final, internal soul survived death and would eventually be reincarnated in the form an animal. When the animal died, the soul would be reincarnated again into a smaller animal and on and on until it final dwindled into nothingness. Until then, however, the spirits of the dead were things to be respected and, at times, feared. The living paid their respects through offerings of food and tobacco, and, in return, the dead could provide prophetic or clairvoyant insight. A soul could be untimely separated from the body, causing illness and requiring a spiritual specialist to recover it.

On rare occasions, human sacrifices were performed. Upon the death of the certepe - the Calusa leader- or the certepe's child such sacrifices were made. If we can draw a parallel to similar practices elsewhere in the Southeast, this would be to provide the deceased with an entourage for aid and comfort in the land of the dead. For the certepe himself, the sacrifices were drawn from his servants in life; for his child, the sacrifices were drawn from other children. Again, if this practice was similar to related traditions in the area, the children sacrificed were probably those dedicated to the service of the certepe's child, destined from birth to serve the certepe's child in this life and the next. Another sacrifice seems to have occurred to sanctify peace treaties. An annual sacrifice of a captive (Fontaneda says Christian captive, but the religion of the captive was almost certainly irrelevant) is also mentioned.