BACKGROUND: The Wnt gene family plays pivotal roles in a variety of biological processes including cell proliferation and differentiation, apoptosis, and embryonic development. Identifying the Wnt signaling pathway in abalone could provide a basis for elucidating growth and development mechanisms and improving quality. OBJECTIVE: To identify the number, protein physicochemical properties, gene structure, phylogenetic analysis, and expression profiles of the Wnt gene family in abalone. METHODS: A comprehensive genome-wide analysis was performed to identify the Wnt gene family in the genomes of three abalone species (Haliotis discus hannai, H. rubra, and H. rufescens). RESULTS: Ten single-copy Wnt genes were identified in each abalone species, suggesting that the number of Wnt genes was relatively conserved in Haliotis. Eight Wnt gene subfamilies, including Wnt1, Wnt4, Wnt5, Wnt6, Wnt7, Wnt10, Wnt16, and WntA, are present in all three species. Each abalone species contains two species-specific subfamilies (Wnt9 and Wnt11 in H. discus hannai, Wnt2 and Wnt11 in H. rubra, and Wnt2 and Wnt9 in H. rufescens), reflecting polymorphisms of the Wnt genes in Haliotis. Interestingly, gastropods are characterised by the loss of Wnt8, suggesting a potential evolutionary specificity in gastropods. As expected, Wnt3 is absent in all protostomes, including the abalone. In addition, spatio-temporal expression profiling revealed differential expression levels of the Wnt genes at different developmental stages and in different tissues of H. discus hannai. HdWnt5 and HdWntA might participate in several processes during larval development stages, including germ layer formation and body axis elongation. HdWnt5 may be involved in eye and tentacle development. HdWnt10 may be related to muscle development, and HdWnt6 may be involved in shell formation in abalone. CONCLUSION: To our knowledge, the results of this study, which is the first genome-wide investigation of the Wnt gene family in abalone, lay the groundwork for future research on the evolution and function of the Wnt gene family in Gastropoda.