Abstract: 【Objective】 The study aimed to analyze the genetic diversity of Coffea arabica germplasm resources using specific-locus amplified fragment sequencing（SLAF-Seq） technology. It identified the genetic backgrounds of local coffee germplasms, providing a theoretical basis for the breeding of new C. arabica varieties. 【Method】 The phylogeny, population genetic structure and principal component analysis were carried out through SNP markers using SLAF-Seq technology based on 40 C. arabica germplasms and 4 non-C. arabica germplasms（served as out-group control）. 【Result】 The sequencing of all tested Coffea sp. germplasm resources yielded a total of 220.54 Mb of data. The average number of reads of sequencing sample was 5012189, with an average Q30 of 95.90%, and an average GC content of 39.48%. The percentage of clean reads localized to the reference genome constituted an average of 95.05% of all clean reads. A total of 214254 SLAF tags were detected from 44 coffee germplasm resources, with an average of 140742 SLAF tags per sample.The number of SLAF tags distributed in each sample ranged from 46234 to 171026. A total of 1186433 population SNP molecular markers were developed, with the number of SNP molecular markers per sample ranging from 381105 to 903823, the integrity of SNP markers ranging from 32.12% to 76.18%, and heterozygosity rate from 6.23% to 17.49%.The distribution of SNP in C. arabica showed some regional concentration, primarily on the chromosome set from 1c to 11c derived from one of the parents, C. canephora（Robusta coffee）. The results of phylogeny, population genetic structure and principal component analysis displayed that the groups of C. arabica Typica type, groups of C. arabica Bourban type, and the groups containing Catimor were clearly distinguished from each other and the genetic backgrounds of 18 C.arabica germplasms were clarified. 【Conclusion】 The 40 C. arabica germplasms in the study are mainly divided into Typica type group, Bourbon type group and the group containing Catimor comercial germplasm. The genetic diversity of C. arabica resources can be accurately analyzed based on SNP molecular markers developed by SLAF-Seq technology.