Many populations of species belonging to the order Crocodilia are threatened because of habitat loss and degradation, parasitic diseases, illegal trafficking, and indiscriminate hunting. Although several studies have revealed that crocodiles, caimans, and alligators are frequently infected by Hepatozoon species, the results from studies exploring the costs of these apicomplexan parasites on their reptilian hosts are still scarce and with inconclusive results. Here, we molecularly assessed the prevalence and genetic diversity of Hepatozoon spp. to explore the differences in body condition in captive individuals of two species of neotropical crocodilians with conservation threats, the spectacled caiman (Caiman crocodilus) and the American crocodile (Crocodylus acutus). Fourteen percent of spectacled caimans were infected by Hepatozoon caimani, whereas no American crocodiles showed infection. The prevalence of Hepatozoon in spectacled alligators varied along age, where subadult individuals were the most frequently parasitized. Surprisingly, the body condition of infected individuals was significantly higher than the body condition of uninfected spectacled caimans, which suggests greater negative effects of the infection in individuals with poor quality. Also, the body condition of subadult individuals was significantly higher than the body condition of juveniles of both alligator species, likely reflecting differences in the occupancy of habitats with higher resource abundance or variations in the nutritional values of the diet between these age classes. These outcomes provide valuable information on disease ecology for developing conservation strategies and the management conservation of wildlife populations of these species.