Understanding phylogenetic relationships and genetic diversity in $Citrus$ are important in clarifying genetic relationships, characterizing germplasm and the registration of new cultivars. There are some $Citrus$ accessions in Iranian citrus collections which have been classified merely based on their morphological traits. Molecular markers would help to infer their relations with known cultivars. In this study 30 $Citrus$ accessions and eight known cultivars from Kotra collection were investigated using 11 pairs of SSR markers, which in total produced 63 alleles with an average of 5.72 alleles per locus. The lowest number of alleles was observed in cAGG9 locus with only 2 alleles and the highest number of alleles was observed in TAA41 locus with 10 alleles. All loci had pretty high PIC with an average of 0.571. The highest PIC was related to TAA41 locus with 0.745. A similarity dendrogram was constructed using Complete Linkage clustering method which put the 38 samples into 5 major groups.