From October 1986 to January 1987, feces from 119 Caiman yacare and 12 Caiman latirostris were collected in Paraguay and later examined for coccidian oocysts; 69 of 119 (58%) samples from C. yacare and 3 of 12 (25%) samples from C. latirostris contained coccidian oocysts. Two eimerians infected C. yacare and both are described as new species. Sporulated oocysts of Eimeria paraguayensis n. sp. are ellipsoid, 34.0 x 23.6 (26-38 x 20-29) microns with sporocysts ovoid, 14.0 x 7.1 (10-19 x 6-10) microns. Sporulated oocysts of Eimeria caimani n. sp. are spheroid, 22.4 (19-29) microns with sporocysts ovoidal, 12.9 x 6.5 (8-17 x 5-8) microns. Isospora jacarei infected C. latirostris and is redescribed. Sporulated oocysts of I. jacarei are sub-spheroid, 13.2 x 12.1 (10-18 x 10-15) microns with sporocysts ellipsoid, 10.4 x 5.8 (7-13 x 4-11) microns. To date, members of the Eimeriidae found in Crocodylia include 5 species of Eimeria and 2 of Isospora including the new species described here.