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The spotted seal (Phcoa largha) is the only pinniped species reproducing in the wild in China. Wild populations of this species have declined sharply in China due to anthropogenic impacts. Forty-six individuals died accidentally in Liaodong Gulf between 2018 to 2020 and were collected. The genetic diversity and population structure of this population were investigated using mitochondrial ND4L and D-loop sequences, and the results were compared with the same population in 2005. The haplotype diversity of Liaodong Gulf spotted seals was low compared to other spotted seal populations in other habitats. Fortunately, the genetic diversity of the current Liaodong Gulf spotted seal population was higher than 15 years ago, and the population expanded between 2005 and 2020. Our findings indicated that conservation activities for Liaodong Gulf spotted seals in recent decades have been valuable, and should persist in the future.