Abstract: Hexosaminidase (-Hex, EC 3.2.1.52) is one of glycosidases, have been shown to be universally distributed among most types of living organisms.Hexosaminidase family genes in Cucumis melo were genome-wide analyzed and 5 members of Hex family genes were found in the melon genome database. With the analysis of protein structure prediction software such as Pfam, we removed 2 incomplete genes and filtered out 3 genes in C. melo. These protein sequences were analyzed by multi -sequence aligned, which were similar in Arabidopsis thaliana, Capsicum annuum, Solanum lycopersicum, Theobroma cacao, Setaria italica, Vitis vinifera, C.sativus and C.melo. The structure evolution relation and conserved motifs were researched by bioinformatics method. The results indicated that this gene family was highly conservative with same motifs in the same 茁-Hex family. Each Hex family within phylogenesis tree demonstrated a bit of differences and the major domain were conserved too.