Inter- and intracellular cysts from a presumed single species, Myxobolus procerus (Kudo, 1934), parasitising the trout-perch Percopsis omiscomaycus were compared with respect to their spore morphology and small subunit 18S ribosomal DNA. The two cyst types have similar pyriform spores and comparable ranges in spore length and width, size of the polar capsules and number of filament coils. However, fixed spores of the intracellular cysts are significantly shorter (p<0.05) in mean length than those from intercellular cysts, giving them a broader appearance. Comparing 991 base pairs of 18S rDNA revealed a 20 bp difference between the two cyst types (97.9% similarity), 10 due to base substitutions and 10 due to the presence or absence of a base. The described morphological differences and consistent 2.1% difference in the 18S rDNA reveal that the intracellular form is a separate species, which is described herein as Myxobolus intramusculi n. sp. M. intramusculi n. sp. and M. procerus may be sister species and it is suggested that the two species arose through sympatric speciation involving a switch in site specificity within a single host species.