It is necessary for mine countermeasure systems to recognise the model of a water mine before destroying because the destroying measures to be taken must be determined according to mine model. In this paper, an immune neural network (INN) along with water mine model recognition system based on multi-agent system is proposed. A modified clonal selection algorithm for constructing such an INN is presented based on clonal selection principle. The INN is a two-layer Boolean network whose number of outputs is adaptable according to the task and the affinity threshold. Adjusting the affinity threshold can easily control different recognition precision, and the affinity threshold also can control the capability of noise tolerance.