Freshwater turtles from 28 species representing 6 families, categorized as “wild,” “captive,” or “wild-caught, captive-raised,” were analyzed for the presence of intraerythrocytic, parasitic protozoa. Microscopic analyses of blood smears from 327 individual turtles revealed parasites in the blood of 29% of these individuals (n = 96), with levels of parasitemia ranging from 0.003% to 2.1%. SYBR ^® Green–based quantitative polymerase chain reaction confirmed these results with 29% overall prevalence (94 of 324), with 66% prevalence in the Geoemydidae, 26% prevalence in the Emydidae, and 23% prevalence in the Kinosternidae. No infections were detected in members of the Chelidae, Pelomedusidae, and Trionychidae. Prevalence was highest in wild turtles with 67%–100% from 7 locations, followed by wild-caught, captive-raised turtles with 4%–26% from 2 locations, while detections in captive turtles were zero in 2 locations and 3% in the remaining third location. Comparative sequence analyses of 583-bp amplicons of 18S rRNA gene fragments allowed us to identify 80 Haemogregarina infections and one Hemolivia infection. Parasites representing the genus Hepatozoon were not detected. Because parasites were generally detected in wild turtles and only rarely in captive turtles, captive breeding with subsequent release of turtles would seem to pose little risk to free-ranging turtles with regard to the spread of these parasites. On the contrary, wild turtles would be more likely sources of parasite transmission to captive populations if used in breeding programs.