Four yeast strains were isolated from the gut of stingless bee, collected in Churdhar, Himachal Pradesh, India. Physiological characterization, morphological examination, and sequence analysis of small subunit ribosomal RNA (18S rRNA) genes, internal transcribed spacer (ITS) region, and D1/D2 domain of the large subunit rRNA gene revealed that the four strains isolated from the gut of stingless bee belonged to the Debaryomyces clade. Strain CIG-23H showed sequence divergence of 7.5% from Debaryomyces nepalensis JCM 2095, 7.8% from Debaryomyces udenii JCM 7855, and Debaryomyces coudertii JCM 2387 in the D1/D2 domain. In the ITS region sequences, strain CIG-23H showed a 15% sequence divergence from Debaryomyces nepalensis JCM 2095 and Debaryomyces coudertii JCM 2387. In 18S rRNA gene sequence, the strain CIG-23H showed 1.14% sequence divergence from Debaryomyces nepalensis JCM 2095 and and Debaryomyces coudertii JCM 2387, and 0.83% sequence divergence from Debaryomyces hansenii NRRL Y-7426. Strain CIG-23H can utilize more carbon sources than closely related species. The findings suggest that strain CIG-23H is a novel species of the genus Debaryomyces, and we propose to name it as Debaryomyces apis f.a., sp. nov. The holotype is CBS 16297, and the isotypes are MTCC 12914 and KCTC 37024. The MycoBank number of Debaryomyces apis f.a., sp. nov. is MB836065. Additionally, a method using cresol red and Bromothymol blue pH indicator dyes was developed to screen for lipase producers, which is more sensitive and efficient than the currently used phenol red and rhodamine B dye-based screening methods, and avoids the problem of less differentiable zone of hydrolysis.