Cladistic analysis of nucleotide characters derived from partial 18S rDNA sequences has been used to infer phylogenetic relationships among five Candida species that exist in nature strictly as intracellular gut endocytobionts of anobiid or cerambycid beetles. Concordant with their assumed taxonomic status, all five species resolve within Saccharomycetales. For both the anobiid-derived taxa, C. ernobii, C. karawaeiwii and C. xestobii, and the cerambycid-derived taxa, C. tenuis and C. rhagii, this phylogenetic position clearly discriminates Candida yeasts from the anobiid yeast-like endocytobionts in Symbiotaphrina which resolve within filamentous ascomycetes. The analyses provide no evidence for a discrete lineage of Candida endocytobionts within Saccharomycetales. Rather, each of the anobiid symbionts and the cerambycid-derived species resolve in separate clades. These data confirm the polyphyletic origins of intracellular symbioses between ascomycetes and Coleoptera and provide another example of convergent evolution in fungal-arthropod associations. The implications of the phylogenetic data for theories on the origins of endocytobiosis are discussed.