Abstract: The isolation of Rhinolophus affinis from Guangdong and Hainan near the Qiongzhou Strait, and the differences in climate and landscape between the South of China and Sichuan Province, prompted our study of morphological divergence. We obtained data on 23 external characteristics and 22 skull characteristics, and the data of 12 external characteristics and 22 skull characteristics was analyzed with SPSS12.0. Principal components and discriminant analyses revealed there were distinct differences both in the external morphological measurements and in the skull measurements among Rhinolophus affinis in Sichuan, Guangdong and Hainan Province. These data suggest that there are three subspecies of Rhinolophus affinis, I.e, R. a. himalayanus Anderson, 1905, R. a. macrurus Anderson, 1905 and R. a. hainanus J Allen, 1906.