<p>Integrated Aquaculture Wastewater Bioremediation Systems (IAWBSs) are crucial for treating nutrient-rich mariculture water. However, there is a lack of detailed information about the functional mechanisms between nitrogen (N) and phosphorus (P) functional genes and the bacterioplankton community in the presence of photosynthetic bacteria (PSB). This study evaluated the connections between N and P functional genes in IAWBSs under the influence of PSB. The results showed significant improvements in effluent quality, with removal efficiencies of 79, 74, 83, 90, and 71% for NO₂⁻−N_, NO₃⁻−N, PO₄³⁻_-P, NH₄⁺−N, and COD_Mn, respectively. Adding PSB enhanced and altered microbial diversity within the system, promoting the abundance of functional genes related to N and P cycling. Notably, genes associated in denitrification (<i>nirK</i> and <i>nirS</i>), ammonification (<i>ureC</i>) and <i>amoB</i>, involved in nitrification, were significantly increased after PSB was added. Furthermore, genes such as <i>phnK</i>, <i>phoD</i>, and <i>phoX</i>, which are involved in P transformation, also showed increased abundance levels. These genes were closely linked to the microbial community distribution, species diversity, and nutrient cycling. Microbial community changes can result in changes in functional gene abundance. This study provides important and novel insights for developing bioremediation strategies for polluted sites. This demonstrates the fundamental relationships between the IAWBSs’ functional units and the distribution of microbial communities under the influence of PSB.</p>