The Florida puma population in southern Florida, United States is one of the best studied felid populations in the world. Since the 1980s, this population has been listed as an endangered subspecies or population of Puma concolor, and the conservation efforts since their rediscovery have allowed the population to rebound from ~20 individuals to ~200 individuals. Previously, a high prevalence of piroplasms was reported from Florida pumas (Puma concolor coryi) from southern Florida. In the current study, we provide biological, morphological, serological, and molecular data on a novel Babesia species. This study also describes the diversity and natural history of ectoparasites on Florida pumas. From January 1989 to May 1993 and January 2000 to April 2014, ectoparasites were collected from free-ranging and captive pumas. Ectoparasites from a total of 262 puma records included six ixodid tick species, one mite (Lyxacarus sp.), a Hippoboscid fly (Lipoptena mazamae), and a flea (Ctenocephalides felis). A live-engorged transmission study of ticks removed from pumas detected the transovarial transmission of a Babesia sp. The Major Histocompatibility Complex (MHC) is a component of the adaptive immune system involved in self/non-selfrecognition and disease susceptibility. Some endangered species maintain high genetic diversity at the MHC despite repeated population bottlenecks. Using next-generation sequencing (Roche 454 and Illumina MiSeq), we determined the allelic diversity of the MHC I and II in Florida pumas respectively. It is currently unclear from our data if the Florida puma MHC was affected by the introgression event. Because most felid species are threatened or endangered, these collective data could have important implications for wild felid conservation.