In recent years, the neurotoxin β-N-methylamino-L-alanine (BMAA) has been reported in some marine mollusk species. To further discover BMAA in marine animals, a total of 59 samples belonging to 3 phyla, 22 families, and 43 species, were collected from Dalian, Rongcheng, and Zhoushan cities, China, in April 2017. All samples were quantified by a hydrophilic interaction liquid chromatography-tandem mass spectrometry (HILIC-MS/MS) analysis of underivatized extract, and ten samples were also analyzed by a liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) analysis using a precolumn AQC (6-aminoquinolyl-N-hydroxysuccinimidyl carbamate)-derivatization method. Results indicated that 48 mollusk samples contained BMAA with concentrations above the limit of detection (0.31 μg g−1 wet weight), and the isomers of BMAA, β-amino-N-methylalanine (BAMA) and 2,4-diaminobutyric acid (DAB) were universally present in most samples. However, N-(2-aminoethyl) glycine (AEG) was not found in any sample. Comparison of both analytical methods showed that BMAA and BAMA were not completely separated by the HILIC column although they still could be identified by specific transitions. In contrast the C18 column provided good separation for the AQC-derivatives of BMAA and all of its isomers. Development of analytical methods and stable isotope tracing of BMAA should be carried out in the future.