Simple Sequence Repeats (SSR) were surveyed in citrus BACEnd sequence (BES) for the development of new SSR markers to extend and saturate existing genetic map.22 403 SSRs with 1～6 bp motif were identified in 46 339 citrus BESs retrieved from NCBI.The estimated frequency of SSRs was approximately 1/1.25 kb,nearly twice the frequency found in Citrus Expressed Sequence Tags.323 primers were selected in the present mapping study,of which 40 were mononucleotide repeats,184 dinucleotide repeats,99 trinucleotide or above repeats.Polymorphism tests showed that 316 primerpairs (98%) could be amplified successfully and 173 pairs (55%) were polymorphic.Among the polymorphic primers,15 pairs were of mononucleotide repeats,100 pairs of dinucleotide repeats,58 pairs of trinucleotide or above repeats.A new linkage map was produced by combining the segregating data of new markers and markers in the previous map.When compared with the published map,the new map integrated 334 SSR markers,9 linkage groups and covered 844.2 cM of citrus genome with an average genetic distance standing at 2.53 cM.The results demonstrated that citrus BES was good for SSR marker development and the developed markers were useful in extending and saturating the citrus genetic maps.So this will provide a reference for development of other species SSR markers and lay a good foundation for citrus gene mapping,mapbased cloning and markerassisted breeding.