The West Indian manatee Trichechus manatus is divided into 2 subspecies: the Antillean (T. m. manatus) and Florida (T. m. latirostris) manatees. This study reports sample prevalence of manatee parasites from populations of these 2 subspecies in different geographical locations. Although necropsy is a valuable diagnostic tool for parasite infections, the need for antemortem diagnostic techniques is important. Fecal samples collected during necropsies of Antillean manatees (n = 3) in Puerto Rico and Florida manatees (n = 10) in Crystal River, Florida, as well as from live-captured Florida manatees (n = 11) were evaluated using centrifugal flotation with sucrose and ethyl acetate sedimentation to compare parasites from each of the populations. Although both fecal examination methods provided similar results, the centrifugal flotation method required less time for diagnosis. The most common parasite eggs found in both populations included the trematodes Pulmonicola cochleotrema and Nudacotyle undicola, oocysts of the coccidian Eimeria spp., and eggs of the ascarid Heterocheilus tunicatus. Eggs of the trematode Chiorchis groschafti were found in both populations of manatees; however, eggs of a related species, Chiorchis fabaceus, were abundant in the Florida samples, but not found in Puerto Rico populations. Trematode eggs of Moniligerum blairi were found in both populations, but were more common in the Florida manatee (42%) than the Antillean manatee (33%). To our knowledge, this is the first report of both Eimeria manatus and Eimeria nodulosa oocysts in Antillean manatees from Puerto Rico.