| Fish of genus Lutjanus Bloch, which are primarily inhabitants of shallow coral reefs, are distributed throughout the tropical and subtropical oceans worldwide. Some species of snappers are important fishery resource and have been cultured in South China Sea. For the morphological characters of genus Lutjanus being very conservative and simple, taxonomists often are confused and problematic by the subtle differentia of pigmentations, coloration pattern. Breeding have been developed through controlled mating and selection of offspring for desirable traits without clearly information of genetic diversity. For protecting the species diversity and genetic diversity of genus Lutjanus this study confirmed the phylogenetic relationship and genetic diversity of familiar snappers (L. russellii, L. erythropterus, L. argentimaculatus, L. stellatus, L.johnii, L.sebae, L.fulvus, L.fulviflamma, L.vitta, L.ophuysenii, L.malabaricus and L.bohar) through the analysis of mitochondrial DNA and microsatellite DNA. The main results in this paper were presented as follows:1. L. russellii mitochondrial genome has been determined with long-PCR. A comparison of this mitochondrial genomic sequence with those of the vertebrate mitochondrial genomes reveals a similar gene order and compact genomicorganization. The encoded genes for 22 tRNAs, two ribosomal RNAs, and 13 encoded genes for proteins in the mitochondria are highly homologous to other ichthyic counterparts. It is the first complete mtDNA sequences of genus Lutjanus in GenBank that have been reported.2. This study evaluated phylogenetic relationship of snappers based on the analysis of complete sequences of the mitochondrial cytochrome b (cytb) gene and COⅡgene in 12 species (L. russellii, L. erythropterus, L. argentimaculatus, L. stellatus, L. bohar, L. johnii, L. sebae, L. malabarius, L. fulvus, L. fulviflamma, L. vitta and L. ophuysenii), which supported the morphological classified system. The length of eytb gene and COⅡgene were 1l41bp and 690bp, respectively. In this study, the phylogenetic relationships from mtDNA data are consistent with the Allen's morphology-based system. Body depth and band pattern show stronge correlation with topologies, consistent with other coral reef fish, and also correspond well to the grouping of species in the Allen's morphology-based system rather than that of Cheng. For instance, L. argentimaculatus, L. erythropterus, L. malabarius and L. sebae have close affinities. Morphologically, the body colors of these four species adults are red and their bodies are relatively deep; in addition, the body sizes of adults are much larger among the genus Lutjanus. The South China Sea is the living space of the two similar species, L. erythropterus and L. malabarius. It was inferred that L.sanguineus depicted in "Information System of Chinese fishes" was synonyms of L. erythropterus or L. malabarius. The highly homologous between L. vitta and L. ophuysenii indicated that there was a relatively shorter time span of genetic differentiation. The result of phylogenetic relationship based on cytb gene and COⅡgene being not coherent absolutely may be conferred to the different velocity of evolution. The combined, data of cytb and COⅡgene sequences testified cytb gene was one of very good gene in mtDNA for evaluation of phylogenetic relationship.3. Thirty-seven microsatellite loci were rapid isolated from the genomic library of L. russellii with PCR, with more than 7 repeat times. The genetic diversity of L. russellii population was analyzed with the 37 microsatellite DNA markers. The average expected heterozygosity, average observed heterozygosity and Hardy-Weinberg departure of 24 loci under Hardy-Weinberg equilibrium in L.russellii were 0.754, 0.754 and zero, corresponding. Cross-species isolations with those markers were carried out for 9 familiar species of snappers (L. erythropterus, L. argentimaculatus, L. stellatus, L. johnii, L. sebae, L. fulvus, L. fulviflamma, L. vitta and L. ophuysenii), and the genetic diversities were also evaluated. The average expected heterozygosity, average observed heterozygosity and Hardy-Weinberg departure under Hardy-Weinberg equilibrium in 9 species of snappers were 0.730～1.000, 0.716～0.915, -0.002～-0.214, corresponding. The data of heterozygosity indicated that the genetic diversities of genus Lutjanus were in a relatively high level. In addition, the heterozygotes were absent in all research species expect L. russellii. The prevalent absence of heterozygotes indicated that there were gene flows in fishes of genus Lutjanus Bloch.
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