Ten yeast strains acquired from different sources and capable of utilizing vegetable oil or related compounds (fatty acid or oleic acid) as sole carbon sources were inoculated into a sequencing batch reactor (SBR) for the treatment of high-strength vegetable oil-containing wastewater. The SBR system stably removed >89% of chemical oxygen demand (COD) and >99% of oil when fed with wastewater containing 15 g/L COD and 10 g/L oil in average. Denaturing gradient gel electrophoresis of polymerase chain reaction-amplified 26S rRNA genes showed that among the ten yeast strains, only Candida lipolytica, Candida tropicalis, and Candida halophila were dominant in the system. To elucidate the major factors affecting the selection of yeast strains in the SBR system, the three dominant strains were compared with two non-dominant strains in terms of COD removal performance, biomass yield, cell settleability, cell flocculation ability, cell emulsification ability, and surface hydrophobicity. Results showed that hydrophobicity and emulsification ability of yeast cells were the two most important factors determining the selection of yeast strains in the treatment of high-strength oil-containing wastewater.