Abstract: Based on the transcriptome sequencing data of flesh of a new longan cultivar‘Xiangcui’，this study developed the novel EST-derived SSR markers to access their applicability on the 4 relative plants （Sapindus mukorossi，Rambutan，Litchi chinensis and Dimocarpus confinis）and then explored the genetic relationship among the 55 germplasms of 5 genera of Sapindaceae family. The results showed that a total of 6 683 SSR loci were mined from 13 934 unigenes with a frequence of 47.96% and mean distance of 4.48 kb. The most abundant type of repeat motif was single nucleotide（52.78%），followed by dinucleotide（26.25%）and trinucleotide（20.19%）. 4 670 pairs of SSR primers were designed and 185 pairs of primers with different repeat motifs were randomly selected for further verification. Of all，the effective PCR success rate shared 78.92%（146 pairs），polymorphism rate shared 34.25%（50 pairs），polymorphic band rate ranged from 50% to 100%. And the rate of longan polymorphic primers transferring to S. mukorossi Gaertn.，N. lappaceum Linn.，L. chinensis Sonn. and D. confinis H.S.Lo were 38.30%，38.30%，68.09% and 74.47%，respectively. Furthermore，with the genetic similarity coefficient of 0.561，UPGMA clustering analysis divided the 55 germplasms into 5 groups，including longan，longli，litchi，Sapindus，and Nephelium.

Key words: Sapindaceae, Dimocarpus longan, SSR, transcriptome