Sequences representing approximately 1,700 base pairs of the 18S rRNA gene from 10 different species in the genus Myxobolus were found to group them into 3 clusters that showed little correlation with spore morphology and size or host specificity, criteria currently used for both higher and lower taxonomic placements in the Myxozoa. Of the phenotypic criteria examined, tissue tropism was most correlated with the rRNA groupings observed. Spores of similar size and shape (Myxobolus cerebralis vs. Myxobolus squamalis) were distantly related in some instances, whereas spores with divergent morphology and size were sometimes found to be closely related (M. cerebralis and Myxobolus insidiosus). These initial investigations into the phylogenetic relationships of putative members of the genus Myxobolus clearly indicate the potential limitations of groupings based on size and morphological properties of the spores and host species infected. We propose that 18S rRNA gene sequences, combined with information on tissue tropism, host species infected, and developmental cycles in the fish and alternate host (when and if known) be given greater consideration in taxonomic placements of myxosporeans.