Candida auris,Candida blankii, andKodamaea ohmerihave been regarded as emerging fungal pathogens that can cause infections with high mortality. For genotyping ofC. auris, a multilocus sequence typing (MLST) scheme based on four locus sequences has been reported, while there is no typing scheme forC. blankiiandK. ohmeri. In the present study, the existing MLST scheme ofC. auriswas modified by adding more locus types deduced from sequence data available in the GenBank database. Furthermore, MLST schemes ofC. blankiiandK. ohmeriwere developed using the four cognate loci (ITS,RPB1,RPB2, D1/D2) and similar sequence regions to those ofC. auris. These MLST schemes were applied to identify the ST (sequence type) of clinical isolates ofC. auris(n= 7),C. blankii(n= 9), andK. ohmeri(n= 6), derived from septicemia or otomycosis in Bangladesh in 2021. All theC. aurisisolates were classified into a single ST (ST5) and clade I, having a Y132F substitution in ERG11p, which is associated with azole resistance. Similarly, all theC. blankiiisolates belonged to a single type (ST1). In contrast, sixK. ohmeriisolates were assigned to five types (ST1-ST5), suggesting its higher genetic diversity. These findings revealed the availability of MLST schemes for these three fungal species for understanding their clonal diversity among clinical isolates.