Two strains representing a yeast species of Metschnikowia were isolated from the surface of citrus leaves collected in Chongqing Province, China. Preliminary tests showed that this species has a biocontrol potential for inhibiting citrus green mold. This yeast species is most closely related to Metschnikowia koreensis based on the phylogenetic tree derived from neighbour-joining analysis of 26S rRNA gene D1/D2 domain. However, M. koreensis differs from this species by seven (1.5%) substitutions in the 26S rRNA gene D1/D2 domain and by >100 (>25%) mismatches in the internal transcribed spacer (ITS) region. The name Metschnikowia citriensis sp. nov. (type strain FL01T=CICC 33213T=KCTC 27796T, strain FL02=CICC 33214) is proposed for the novel species because of morphological, physiological and biochemical characteristics and the sequence comparisons of the 26S rRNA gene D1/D2 domain and ITS region.