Technology of water microorganism recognition plays a key role in water quality detection and fields related. The paper presents a new water microorganism recognition algorithm based on BP neural network classifier technology and genetic algorithm. First, the structure of the presented BP neural network algorithm is analyzed and designed based on the analysis of the requirement of water microorganism recognition system. Second, in order to speed up algorithm calculation and simplify algorithm structure, genetic algorithm is used to improve ordinary BP neural network algorithm, and some specific measures are taken, and the calculation procedures of improved algorithm are redesigned. Finally, the realization and experiment results show that, compared with some methods which have relatively high accuracy, the algorithm can improve water microorganism recognition accuracy, decrease the calculation time needed greatly and can satisfy the engineering requirement in water microorganism recognition.