Abstract:This study investigated population genetics and phylogenetics of Liniparhomaloptera disparis (Cypriniformes: Homalopteridae) among river drainages on Hainan Island and in coastal western South China, using nucleotide sequences in the mtDNA control region. Samples were taken from 3 major river systems on Hainan Island (Province), 2 major branches of the Pearl River system in Guangdong Province, and 7 independent coastal river systems in Guangdong and Guangxi Provinces. Hainan Island and coastal western South China were connected at the last glacial maximum about 10 thousand years ago. This study thus contributes to the understanding of phylogeography of different fishes from Hainan Island and the South China mainland. A total of 87 individuals from these 12 drainages were used in sequencing; we found 95 variable nucleotide sites among 477 base pairs, with 39 singleton sites and 56 parsimoniously informative sites.Neighborjoining (NJ) analysis with 20 haplotype nucleotides in the control region revealed 3 monophyletic clades. The Pearl River system and the independent coastal drainages in western Guangdong Province are closely related (clade I); the independent coastal drainages in eastern Guangxi Province group tightly with the Changhuajiang River on Hainan Island (clade II); the Wanquanhe and Nandujiang River drainages on Hainan Island form a lineage distinctly separate from the others (clade III). This indicates that populations of L. disparis on Hainan Island are genetically differentiated into 2 lineages, one similar to those in Guangxi Province, and the other unique. The variation within a clade (0.583%-1.775%) was much lower than that between clades (4.205%-5.715%) or that between clades and outgroups (11.825%-13.73%), demonstrating that L. disparis in these 12 drainage systems in coastal western South China and Hainan Island has divided into 3 genetically distinguishable groups. Analysis of molecular variance (AMOVA) revealed that most of the genetic variation resided among populations within a geographic region (65.04%) with little variation between geographic regions (2.24%), rejecting our null hypothesis based on current disjunct geography that populations from the independent drainages in coastal western South China were closely related to those from the Pearl River but distantly related to those from Hainan Island. Variation in the mtDNA control region may have occurred due to drainage separation by montane uplift in the Tertiary, and cannot postglacial disjunction of Hainan Island from the mainland in the Quaternary. This geographic barrier has not existed long enough to effect reproductive isolation, leaving close relationships of populations from the Changhuajiang River on Hainan Island with those from the independent coastal drainages in eastern Guangxi Province. Glacial maxima sea level recessions facilitated connections of different river systems, allowing those from the independent coastal drainages in western Guangdong Province to remain closely related to those from the Pearl River system. Our AMOVA is consistent with the small variation within a clade revealed by the NJ analysis. Speciation within L. disparis and phylogenetic positions among clades require further study.