Abstract: Spatial heterogeneity is an important feature of biological communities in large lakes. Identifying such spatial heterogeneity is helpful for ecological monitoring, assessment and zoning management. Here, to evaluate the spatial difference between the northern and southern zones of Lake Erhai, we investigated monthly dynamics of rotifer community and its environmental and biological variables in the northern and southern zones of Lake Erhai in 2020. Then we compared the diversity and community dynamics of rotifer in the northern and southern zones. A total of 49 rotifers from 25 genera were detected in Erhai Lake throughout the year. A total of 45 rotifers from 23 genera were detected in the northern zone, and 38 species from 19 genera were detected in the southern zone. The species in the southern zone was a subset of species in the northern zone. There was no significant difference in the monthly averaged species richness and true Simpson diversity index of rotifer communities between the two zones. The monthly averaged abundance of rotifers in the southern and northern zones were 487 ind./L and 549 ind./L, respectively. Multiple linear regression analysis showed that there were significant differences in the influencing variables and population dynamics of the dominant species Keratella cochlearis between northern and southern zones, while there was no difference in the influencing variables and the population dynamics of the dominant species Polyarthra dolichoptera between northern and southern zones. According to the Bray-Curtis distance that measured the community dissimilarity, the difference of rotifer species composition between northern and southern zones in December was the largest, with an averaged BC-distance of 0.34. The difference of dominant species was the largest in August, with an averaged BC-distance of 0.73. Redundancy analysis (RDA) showed that temperature and transparency were the critical variables explaining the community structure variation in both the southern and northern zones.