The genetic relationship between Zhaoqing local citrus breeds and other citrus and allied plants was studied using the simple sequence repeat (SSR) molecular marker technique. Among 34 pairs of citrus SSR primers, this study selected 13 primer pairs with high polymorphism to expand 83 bands with 100% polymorphism positive rate. Through cluster analysis, this study effectively differentiated the species, breeds, and even strains of citrus, poncitrus, and atalantia correa. Thus, SSR molecular marker techniques can adapt to the classification of the status research of local citrus germplasm resources. A close genetic relationship was found among Zhaoqing local citrus breeds. This study provided evidence that Citrus haniana Hort. ex Tseng Sihuihanggan is the female parent of C. nobilis Lour. gonggan by combining morphological and other molecular biology research.