To study the biological function of zebrafish ribosomal proteins in response to hypoxic stress, transcriptome analysis was performed on the gill tissues of Danio rerio under hypoxic and normoxic conditions, and the gene expression differences of ribosomal protein family genes in the gill of D. rerio were compared. The results showed that the expression levels of 60 ribosomal protein genes in zebrafish gill tissues were significantly up-regulated at two different concentrations of hypoxia stress, which included 35 large subunit ribosomal protein genes and 25 small subunit ribosomal protein genes. Among the top 15 pathways enriched by the significantly deferentially expressed genes in the zebrafish gills under hypoxia stress, all included the ribosomal protein genes, and 5 were related to ribosomal protein assembly and synthesis. In the enriched “translation” GO term, 44 ribosomal protein genes were included. In addition, the target genes of 60 significantly up-regulated ribosomal protein genes were predicted by two significantly down-expressed miRNA in zebrafish gills under hypoxia stress, which were screened in our previous study. The results show that miR-455-3p can target both ribosomal protein genes rpl13 and rplp1, which might be involved in the adaptation to the hypoxia environment.