In the present study inter- and intra-population species of Lepadella patella were investigated. For this purpose 110 individual of geographical populations of these rotifers were collected from different parts of Arak county, and for each habitat five ecological factors such as longitude, latitude, elevation, temperature and pH were examined. The ANOVA test and also one-sample t-test showed significant difference for morphological characters. In inter- and intra-population section, 10 individual were selected randomly from each populations, then seven quantitative morphological characters were examined, the individuals were separated from other in the PCA plot and UPGMA tree. Significant correlations negative/positive were found between some of morphological characters with studied ecological factors of habitat, in addition variations in morphological characters were seen between population and they were separated in PCA plot and also UPGMA tree. Ecological factors were different between habitat, therefore in this study, we concluded that variation temperature was most effective among all the ecological factors, on diversification of populations.