This study is designed to measure the relative efficiency of regional fishery cooperatives based on Data Envelopment Analysis(DEA) methods. Selecting 40 regional fishery cooperatives in Busan as Decision Making Units (DMUs), the study uses their panel data from 2007 to 2008 to rank the relative efficiency of the DMUs. First, the efficiency score of the DMUs are calculated using CCR, SBM, and super-SMB model. Within the model, input variables are the number of employees and area of fishery cooperatives. Output variables are the amount of deposit money, loan and profit. Based on the efficiency scores calculated from super-SMB model, the efficiency ranking of the DMUs is determined. Second, the differences in average efficiency calculated from the three DEA models are tested using a pair-wise mean comparison test. The results based on the efficiency scores evaluated from super-SMB model show that seven out of the forty DMUs are efficient; among the efficient DMUs, the DMUs that can be benchmarked for inefficient DMUs through the frequency analysis of reference set being identified. Third, the differences in average efficiency of the three DEA models between 2007 and 2008 are tested using pair-wise mean comparison test and the study estimates the efficiency change of the DMUs between 2007 and 2008 using Malmquist productivity index(MPI). Finally, the paper suggests an improved composite DMU superior to the inefficient DMUs evaluated by Super-SBM model.