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Background   Enterocytozoon bieneusi  is a microsporidian, commonly found in animals, including humans, in various countries. However, there is scant information about this microorganism in Australasia. In the present study, we conducted the first molecular epidemiological investigation of  E. bieneusi  in three species of marsupials ( Macropus giganteus ,  Vombatus ursinus  and  Wallabia bicolor ) living in the catchment regions which supply the city of Melbourne with drinking water.    Methods  Genomic DNAs were extracted from 1365 individual faecal deposits from these marsupials, including common wombat ( n  = 315), eastern grey kangaroo ( n  = 647) and swamp wallaby ( n  = 403) from 11 catchment areas, and then individually tested using a nested PCR-based sequencing approach employing the internal transcribed spacer ( ITS ) and small subunit ( SSU ) of nuclear ribosomal DNA as genetic markers.    Results   Enterocytozoon bieneusi  was detected in 19 of the 1365 faecal samples (1.39%) from wombat ( n  = 1), kangaroos ( n  = 13) and wallabies ( n  = 5). The analysis of  ITS  sequence data revealed a known (designated NCF2) and four new (MWC_m1 to MWC_m4) genotypes of  E. bieneusi . Phylogenetic analysis of  ITS  sequence data sets showed that MWC_m1 (from wombat) clustered with NCF2, whereas genotypes MWC_m2 (kangaroo and wallaby), MWC_m3 (wallaby) and MWC_m4 (kangaroo) formed a new, divergent clade. Phylogenetic analysis of  SSU  sequence data revealed that genotypes MWC_m3 and MWC_m4 formed a clade that was distinct from  E. bieneusi.  The genetic distinctiveness of these two genotypes suggests that they represent a new species of  Enterocytozoon .    Conclusions  Further investigations of  Enterocytozoon  spp .  from macropods and other animals will assist in clarifying the taxonomy and epidemiology of these species in Australia and elsewhere, and in assessing the public health risk of enterocytozoonosis.    Electronic supplementary material  The online version of this article (10.1186/s13071-018-2954-x) contains supplementary material, which is available to authorized users.

New operational taxonomic units of Enterocytozoon in three marsupial species