The genetic diversity among 6 Sarcocystis falcatula isolates derived from geographically distinct regions in the U.S.A. was detected using the first internal transcribed spacer region 1 (ITS-1) of the rRNA gene. These sequences were then compared to the full sequence from a Sarcocystis neurona isolate obtained from a California horse diagnosed with equine protozoal myeloencephalitis. No nucleotide differences were detected over partial sequence analysis of 2 additional S. neurona isolates: however, the complete nucleotide sequence for the ITS-1 region was not compared. Twelve nucleotide differences were consistently detected when aligned sequences of S. neurona were compared to those of the S. falcatula isolates. Additional nucleotide base changes were detected among the S. falcatula isolates, but these changes were not consistent in all the S. falcatula isolates. These results indicate that S. falcatula may be comprised of a heterogeneous population and that the ITS-1 region can be used to distinguish S. neurona from S. falcatala used in this study.