A maximal independent set is an independent set that is not a proper subset of any other independent set. Liu [J.Q. Liu, Maximal independent sets of bipartite graphs, J. Graph Theory, 17 (4) (1993) 495-507] determined the largest number of maximal independent sets among all n-vertex bipartite graphs. The corresponding extremal graphs are forests. It is natural and interesting for us to consider this problem on bipartite graphs with cycles. Let \mathscrBₙ (resp. \mathscrBₙ') be the set of all n-vertex bipartite graphs with at least one cycle for even (resp. odd) n. In this paper, the largest number of maximal independent sets of graphs in \mathscrBₙ (resp. \mathscrBₙ') is considered. Among \mathscrBₙ the disconnected graphs with the first-, second-, \ldots, \fracn-22-th largest number of maximal independent sets are characterized, while the connected graphs in \mathscrBₙ having the largest, the second largest number of maximal independent sets are determined. Among \mathscrBₙ' graphs have the largest number of maximal independent sets are identified.