Populus talassica Kom. is an ecologically important species endemic to central Asia. In China, its main distribution is restricted to the Ili region in the Xinjiang Autonomous Region. An understanding of genetic diversity and population structure is crucial for the development of a feasible conservation strategy. Twenty-six high-level simple sequence repeat (SSR) markers were screened and used to genotype 220 individuals from three native populations. A high level of genetic diversity and low population differentiation were revealed.