ObjectiveThis preliminary study was conducted to reveal that the molecular identity of Encephalitozoon spp. and Enterocytozoon bieneusi in indoor domestic cats' fecal samples from Turkey was screened using the PCR.Materials and MethodsNested PCR was performed using MSP and EBITS primers.All of the amplification products were sequenced to identify the microsporidia species.ResultsFour (5.5%) and three (4.1%) genomic DNA isolates of the fecal samples from 72 indoor domestic cats showed amplification of the ITS regions of E. bieneusi and Encephalitozoon spp., respectively. Two different genotypes, D and IV, of E. bieneusi were determined in two cats each based on the ITS sequence analyses. Moreover, Encephalitozoon spp. sequence analyses revealed three isolates belonging to E. intestinalis.ConclusionsThispreliminary study has provided the first molecular data on the zoonotic genotypes of E. bieneusi and E. intestinalis in cats in Turkey. Furthermore, E. bieneusi genotype IV (accession number MG727664) was submitted to GenBank for the first time in the Western Palearctic Region as hosted by a domestic cat. Additionally, E. intestinalis (accession number MG570080) was also submitted to GenBank as a valid ITS sequence for the first time as hosted by a domestic cat worldwide.