Proposed in this paper is a neural network-based method for extracting the relationship between bacteria and their habitats.In this method,implicit senior features are learnt automatically to avoid the complexity and redundancy of the traditional artificial design of features,and,distributed vector representation with rich syntactic and semantic knowledge for words and entities,two different neural network models,as well as integrated document- level extraction results,are comprehensively employed to make an evaluation on the BB-event corpus from BioNLP-ST 2016.Experimental results show that the proposed method achieves preferable F1 score,which means that it is effective in bacteria biotope extraction.