It is postulated that the presence of nypa palm (Nypa palm) in mangrove forest affect the reproductive function of fish by inhibiting the growth of macro invertebrates. The impact of Nypa fruticans (Wurmb) and mangroves on the benthic macro invertebrate community of Andoni River was carried out between January and August, 2017. A total of four stations were chosen based on nypa palm and native mangrove species’ presence and absence, station 1 (Open water), Station 2 (Nypa palm dominance), station 3 (Rhizophora and Avicennia dominance), Station 4 (Mixed). Results of water quality parameters include; pH 6.99±0.16, Temperature 28.20±0.05°C, DO 4.71±0.18mg/L, Conductivity 19.52±0.20µm/s, Salinity 10.76±0.07ppt, TDS 13.45±0.27ppt. Mean values of the physico-chemical parameters (P > 0.05) were not significantly different. Twelve taxa of benthic macro-invertebrates in eleven families were collected. The crustaceans were more in diversity (38.46%), while bivalvia, pisces and oligochaete had the least percentage composition (7.69%). The gastropods were more in species dominance (44.69%), while the Oligochaeta were least in abundance (0.61%). Shannon Weiner’s index across the stations for benthos was highest in station 2 (1.840) and lowest in station 1 (1.103). Simpson’s index was highest in station 2 (1.990) and lowest in station 1 (1.938). Pielou’s index of evenness was highest in station 2 (0.767) and lowest in station 1 (0.616). All the macro-invertebrates recorded were clean water and pollution tolerant species, and showed no significant difference across stations (P>0.05). In conclusion this study indicates that nypa palm does not affect the proliferation of macro invertebrates, which supports fishery population along the food chain.