Study on genetic polymorphism of sixteen accession of hot pepper (Capsicum annuum spp.) provided by AVRDC was assessed using seven microsatellite markers. All of markers used in this study were polymorphic in sixteen pepper varieties. Three to eight alleles were detected for the remaining loci. In total, 40 alleles were detected, of which, 5.15 alleles per one locus on average. The highest number of different alleles was detected with Hpms 1-3 and Hpms 1-172 primers (8 alleles). Average polymorphism information content (PIC) value was 0.76, ranging from 0.63 (Hpms 1-69) to 0.85 (Hpms 1-172). Cluster analysis of the band patterns separated the varieties into two groups corresponding to varietal types. Two accessions AVPP0025 and AVPP0414 had similarity coefficient of 1.00. Resistant genes to anthracnose disease were determined in these varieties, so they can use as parental material for crop improvement program.