Dimocarpus longan, commonly known as the longan, belongs to the family Sapindaceae, and is one of the most economically important fruits commonly cultivated in several regions in Asia. There are various cultivars of longan throughout the Thai-Malay peninsula region, but until now no phylogenetic analysis has been undertaken to determine the genetic relatedness of these cultivars. To address this issue, 6 loci, namely ITS2, matK, rbcL, trnH-psbA, trnL-I and trnL-trnF were amplified and sequenced from 40 individuals consisting of 26 longan cultivars 2 types of lychee and 8 herbarium samples. The sequencing results were used to construct a phylogenetic tree using the neighbor-joining (NJ), maximum likelihood (ML) and Bayesian inference (BI) criteria. The tree showed cryptic groups of D. longan from the Thailand-Malaysia region (Dimocarpus longan spp.). This is the first report of the genetic relationship of Dimocarpus based on multi-locus molecular markers and morphological characteristics. Multiple sequence alignments, phylogenetic trees and species delimitation support that Dimocarpus longan spp. longan var. obtusus and Dimocarpus longan spp. malesianus var. malesianus should be placed into a higher order and are two additional species in the genus Dimocarpus. Therefore these two species require nomenclatural changes as Dimocarpus malesianus and Dimocarpus obtusus, respectively.

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Longan is one of the most economically important fruits of Asian countries belonging to the family Sapindaceae. Essentially, there is a lack of fundamental karyological data on different cultivars in longan although the whole genome of longan has been successfully sequenced. This study is the first to report the chromosome numbers and karyotypes of nine cultivars of the genus Dimocarpus cultivated widely in the northern regions of Thailand. These cultivars are Chompoo, Haew, Phuangthong, Thao, Jumbo, Phuen-Mueang, Pumateenkong, Chuliang (China), Kohala (America), and one of them (Thao, Dimocarpus obtusus, Lithanatudom & Chaowasku, comb. et stat. nov.) is considered as a rare species found in Thailand. The somatic chromosome number of cells derived from the root tip collected from the air layering branch of all cultivars was determined as 2n=2x=30. All cultivars showed a predominance of metacentric chromosomes in each karyotype indicating their symmetric nature. The karyotype of these cultivars was placed into categories 1B and 2B based on Stebbins classification. In addition, we analyzed the scatter diagrams of asymmetry indices, UPGMA dendrogram with fruit morphology, and PCoA graph together with the karyotypic relationship, and overall, the results revealed that all cultivars of the genus Dimocarpus examined can be divided into two major groups.