Abstract： Partial mitochondrial COI gene region of 30 individuals of Soletellina diphos collected from Nanri Island, Fujian. China, were cloned by PCR and directly sequenced from both directions to detect the Single Nucleotide Polymorphism (SNP) among individuals and genetic diversity of the natural population on molecular level. Evidently, the content of (A+T) base in COI was higer than that of (G+C) base, and its average nucleotide percentage composition of T, C, A and G were 41.95%, 16.07%, 18.53% and 23.45%, respectively. According to the mutation form, mutation frequency and mutation distribution, a total of 13 SNP loci were detected in those 655 base pairs of gene fragments, containing 12 transformations and 1 transversion (R=13.04). And 9 haplotypes were found in 30 samples through multi-sequences alignment. One SNP locus located at 203 bp of which was nonsynonymous mutation that caused the change between Leucine and Phenylalanine, while the other 12 variation sites had synonymous mutations after amino acid analysis. There was no distinct relevancy between different SNP loci. Population of S. diphos displayed just slightly higher than standard haplotype diversity index (Hd) of (0.598 0 ± 0.103 0) and relatively lower nucleotide diversity index (Pi) of (0.002 9 ± 0.000 6), with the average nucleotide difference (k) of 1.912 6 based on COI sequences. The Kimura 2-parameter genetic distance between different individuals in the specimen ranged from 0 to 0.009 2, and the total average distance was (0.002 9 ± 0.001 0). Results of both the Tajima’s D and Fu’s Fs neutral tests were not significantly negative, illustrating that the inheritance of this population was relatively stable. Historical test results of seawater samples collected around the area of Nanri Island from April 2008 to December 2018 were detailed analyzed in order to get to know about the habitat conditions of S. diphos through obtaining the seasonal and monthly changing rule of 10 physical and chemical indexes such as salinity, temperature, pH, dissolved oxygen, chlorophyll a, transparency, chemical oxygen demand, inorganic nitrogen, inorganic phosphorus and petroleum. The annual trend of water environment factors data expressed that S. diphos mainly lived in the intertidal zone and shallow water where the range of monthly average seawater salinity, temperature, pH, dissolved oxygen, chlorophyll a, transparency, chemical oxygen demand, inorganic nitrogen, inorganic phosphorus and petroleum was 26.84~34.33, 13.27~29.33℃, 7.89~8.54, 5.64~9.31 mg/L, 0.33 ~15.57 μg/L, 0.40 ~1.79 m, 0.22 ~1.59 mg/L, 0.04 ~0.45 mg/L, 0~0.16 mg/L and 0 ~0.20 mg/L, respectively. The yearly changes of salinity and temperature from spring to autumn rose and then fell, with the highest value in summer. Every spring to summer, pH and dissolved oxygen demonstrated a fluctuation of decrease in the same way. Meanwhile the tendency of inorganic nitrogen decreased first and increased later from spring to autumn, with the lowest value in summer. Except for chemical oxygen demand and petroleum content, the annual changes of the other three factors all showed an obvious or a certain seasonal difference rule. It also indicated that S. diphos could grow and reproduce well under the above physical and chemical conditions of seawater environment in the nearshore area of Nanri Island.