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<jats:title>Abstract</jats:title><jats:p>The giant river prawn, <jats:italic>Macrobrachium rosenbergii,</jats:italic> is an economically important freshwater prawn. The cultivation of zoea larvae is crucial for the success of the <jats:italic>M. rosenbergii</jats:italic> industry. In this study, we surveyed the microbial community diversity and structure associated with <jats:italic>M. rosenbergii</jats:italic> zoeae at different stages of larval development. Samples of zoea larvae from different developmental stages were collected and subjected to high‐throughput DNA sequencing. Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria were the dominant phyla in all six sample groups. At the genus level, the relative abundance of <jats:italic>Bacillus</jats:italic> decreased, and that of <jats:italic>Enterobacter</jats:italic> increased with the growth of the zoeae. This may have been related to the intestinal development of the zoea larvae. The microbial diversity of <jats:italic>M. rosenbergii</jats:italic> zoea larvae decreased significantly with development. The beta diversity analysis showed that the closer the developmental stage of <jats:italic>M. rosenbergii</jats:italic>, the more similar the structure of the associated bacterial communities.</jats:p>