Capsicum diversity is getting lower in modern crops because of the genetic erosion. In Capsicum, breeders have been mainly focused on agriculturally important traits such as disease resistances, high yield and pungency. However, this narrow breeding pool hampered to develop improved cultivars. It has become a hot issue to conservation of genetic diversity and exploitation of wild germplasm in Capsicum. Analysis of genetic diversity and construction of core collection is the first step to make efficient use of germplasm. Although there have been several attempts to construct core collections in Capsicum, most of these works were limited due to handling small number of samples, relying mainly on the characterization of morphological traits or focusing only C. annuum species. To expand understanding of the structure and genetic diversity of germplasm in Capsicum, we need to have a highly efficient genotyping tool to handle large number of samples. Toward this end, we are analyzing 3,599 germplasm accessions including other cultivated species and wild species in Capsicum with 48 single nucleotide polymorphism (SNP) markers.