Abstract:To assess the Xiaoshi Island Apostichopus japonicus national aquatic germplasm reserve, parameters related to the water environment, sediment environment, marine ecology, protected biological resources, and genetic diversity of A. japonicus from 2012 to 2018 were examined. The condition of the reserve was evaluated by several indices, including the single factor pollution index (Pi), organic pollution index (A), biodiversity index (H′), haplotype diversity index, and nucleotide diversity index of the mitochondrial DNA D-loop sequence. During 11 cruises, all of the observed parameters met the seawater evaluation standards, except for the dissolved inorganic nitrogen concentrations, which were greater than the established standards in May 2016 (Pi = 1.08) and August 2017 (Pi = 1.31). This indicates that the water was polluted by organic matter (A = 1.001) in August 2017. The observed sediment parameters met the Class 1 national sediment quality standards. The marine biodiversity indices were high (H′ ≥ 2). However, the phytoplankton diversities were low in May 2016 (H′ = 0.45) and August 2017 (H′ = 0.28), and the small zooplankton diversity was low in May 2018 (H′ = 0.77). The biological resources in the reserve area were rich. The number of A. japonicus per unit square area gradually increased from ~2 to 3~5. A. japonicus genetic diversity was high in 2012 (haplotype diversity index = 0.995, nucleotide diversity index = 0.039) and 2018 (haplotype diversity index = 0.993, nucleotide diversity index = 0.037), and there were no significant genetic differences between the groups. Overall, the marine ecological environment and aquatic germplasm resources in the reserve are well-protected. However, it is necessary to prevent future risks associated with dissolved inorganic nitrogen contamination.