Three yeast strains were isolated from industrial wastes in Thailand. Based on the phylogenetic sequence analysis of the D1/D2 region of the large subunit rRNA gene, the internal transcribed spacer (ITS1-5.8S rRNA gene-ITS2; ITS1-2) region, and their physiological characteristics, the three strains were found to represent two novel species of the ascomycetous anamorphic yeast. Strain JP52T represent a novel species which was named Cyberlindnera samutprakarnensis sp. nov. (type strain JP52T; = BCC 46825 T = JCM 17816T = CBS 12528T, MycoBank no. MB800879), which was differentiated from the closely related species Cyberlindnera mengyuniae CBS 10845T by 2.9 % sequence divergence in the D1/D2 region and 4.4 % sequence divergence in the ITS1-2. Strain JP59 T and JP60 were identical in their D1/D2 and ITS1-2 regions, which were closely related to those of Scheffersomyces spartinae CBS 6059T by 0.9 and 1.0 % sequence divergence, respectively. In addition, supportive evidence of actin gene and translational elongation factor gene by sequence divergence of 6.5 % each confirmed their distinct status. Furthermore, JP59 T and JP60 differentiated from the closely related species in some biochemical and physiological characteristics. These two strains were assigned as a single novel species which was named Candida thasaenensis sp. nov. (type JP59T = BCC 46828T = JCM 17817T = CBS 12529T, MycoBank no. MB800880). © 2012 Springer Science+Business Media B.V.