The purpose of the present study is to investigate the composition of intestinal Candida in community healthy population and emergency intensive care unit (EICU) patients. The stool or rectal swab samples were collected from 1 732 community healthy people in Shanghai between May 2014 and July 2014, and from 191 EICU patients in Ruijin Hospital, Shanghai Jiao Tong University School of Medicine between February 2014 and January 2015. After fungal culture, individual colonies were collected and further identified by amplifying and sequencing of internal transcribed spacers (ITSs). The composition characteristics of intestinal fungi in the two groups were analyzed by statistical method. The results demonstrated that, in the intestinal tract of community healthy population, 9 Candida species were detected. The Candida colonization rate of community healthy population was 13.16%, and the colonization rates of two or three Candida species were 3.81% and 0, respectively. While in the intestinal tract of EICU patients, only 5 Candida species were cultured. The Candida colonization rate of EICU patients was 37.17%, and the colonization rates of two or three Candida species were 9.95% and 2.09%, respectively. The positive rates of common intestinal Candida in community healthy population and EICU patients were Candida albicans (C. albicans) (5.25% vs. 27.23%), C. glabrata (5.83% vs. 13.61%), C. tropicalis (0.52% vs. 7.33%), C. parapsilosis (4.16% vs. 2.09%), C. metapsilosis (1.10% vs. 1.05%). It is concluded that the colonization rate of intestinal Candida in EICU patients is significantly higher than that in community healthy population (P<0.001). The colonization rates of two or three Candida species in EICU patients are also higher than those in community healthy population (P＝0.001, P<0.001). EICU patients have a higher colonization rate of intestinal Candida, to a certain extent, could increase the probability of Candida infection.