The invention provides an aquatic animal SNP marking and selection method, which can solve the problems of low efficiency and high cost existing in the current SNP marking and selection technique. The method adopts the technical proposal comprising the following steps: firstly, genome DNA abstraction; secondly, MseI restrictive enzymes cutting, connection of connecting ends and pre-amplification; thirdly, heterozygous double chain forming, CEL I enzyme cutting and Bst DNA polymerase extending; fourthly, separation of beads containing SNP locus DNA molecule; fifthly, object DNA amplification, concentration and clone sequencing; and sixthly, SNP locus identification. The new SNP marking and selection method can efficiently, plentifully and randomly separate SNP under the condition of unknown genome information, thereby being favorable for the development and the subsequent utilization of the abundant SNP, and having significant application value and popularization prospect in aquatic animal SNP marking and selection, germplasm identification, genetic diversity evaluation, molecular breeding and the like.