Hox genes have been investigated in various Arthropod species, resulting in the identification of ten Hox genes, organized in a colinear arrangement within the genome. Among arthropods, crustaceans exhibit a remarkable diversity of body shapes, which are associated with a variety of egg types, embryonic development patterns, and importantly, with the modulation of Hox genes to specify the identity of body segments along the antero-posterior axis of the embryo. Although there are more than 52,000 species of crustaceans described, their genomic resources are relatively limited, making it challenging to employ several molecular tools for studying embryonic development. In this regard, we present a protocol for identifying Hox genes in a freshwater prawn using degenerate primers and transcriptome analysis. This method enables the study of specific functions of Hox genes, thereby contributing to the evolutionary understanding of the diversity of body shapes in crustaceans.