The genetic diversity of 15 Eulecanium giganteum (Shinji) populations, which were collected from five regions (Hami, Bazhou, Akesu, Kashi and Hetian) of Xinjiang, was investigated by using intersimple sequence repeat (ISSR) markers. The results showed that Shaya population in Akesu had the highest genetic diversity, while Hejing population in Bazhou had the lowest genetic diversity. Correlation analysis showed that the genetic diversity of E. giganteum populations was positively correlated with the annual mean air temperature and humidity, but less correlated with the age of host tree and latitude, and negatively correlated with the elevation. Besides, the genetic distance between the paired populations was positively correlated with the annual mean air temperature. Coccid occurred severely on the south side and middle parts of trees.