The prediction of operons is a critical step for the reconstruction of biochemical and regulatory networks at the whole genome level. In this paper, a novel operon prediction model is proposed based on Markov Clustering (MCL). The model employs a graph-clustering method by MCL for prediction and does not need a classifier. In the cross-species validation, the accuracies of E. coli K12, Bacillus subtilis and P. furiosus are 92.1, 86.9 and 87.3%, respectively. Experimental results show that the proposed method has a powerful capability of operon prediction. The compiled program and test data sets are publicly available at http://ccst.jlu.edu.cn/JCSB/OPMC/.