Phalaenopsis spp., known as 'moon orchid' or 'moth orchid' is one of the most important orchid genera (family Orchidaceae) in the world. This is related to its diversity and popularity as the most popular ornamental plant or cut flower for collectors, breeders and orchid lovers around the world. However, most of the Phalaenopsis spp. currently very difficult to find in the wild, even among them are included in the threatened category. This study aims to analyze the genetic diversity of the Phalaenopsis.spp orchid germplasm indigenous to Kalimantan using a DNA Barcoding (matK) marker. Twelve samples of Phalaenopsis spp., from various regions in the provinces of South Kalimantan (7 species), East Kalimantan (4 species) and West Kalimantan (1 species) have been successfully collected and characterized molecularly. The results showed that in general Phalaenopsis spp. Indigenous Kalimantan has a genetic diversity of 0.013. Meanwhile, the results of the phylogenetic analysis showed that the germplasm was divided into five main clades, in which there were 4 species of clade I, 2 species of clade II, 3 species of clade III, 2 species of clade IV and 1 species of clade V (outgroup).