【Objective】 SSR markers were used to identify and study the genetic diversity of hybrid progenies from crosses of Shatian pummelo as female, which can provide technical and materials’ support and a theoretical basis for innovating germplasm and genetic improvement of citrus. 【Method】 The hybrid nature of 159 offsprings from the two cross combinations of Shatian pummelo was analyzed, and the genetic relationship between parents and offsprings was analyzed with UPGMA. 【Result】 One hundred and three hybrids was identified from 104 F1 seedlings of ‘Shatianyou’ × ‘Chandler’ pummelo by 4 pairs SSR primers, the identification rate was 99.04%, and 70 progenies had non-parent markers in primer AGC9. All the offsprings from ‘Shatianyou’בHongjiangcheng’ were proved to be hybrids with 5 pairs SSR primers, one homozygous maker AAT12 was obtained, and some markers were absent in 55 F1 seedlings in primer GA18 and AGC9. The cluster analysis of SSR data indicated that the genetic variation of hybrids from the two cross combinations was obviously, and the genetic diversity between the two combinations of crosses was obviously different. 【Conclusion】 The identification of hybrids and genetic diversity of citrus can be assessed efficiently by SSR markers, and the cross breeding is an effective way to obtain variant strains.