An individual-based modeling approach to estimate biological reference points for blue crabs (Callinectes sapidus) in Chesapeake Bay offered several advantages over conventional models: (i) known individual variation in size and growth rate could be incorporated, (ii) the underlying discontinuous growth pattern could be simulated, and (iii) the complexity of the fishery, where vulnerability is based on size, shell status (e.g., soft, hard), maturity, and sex could be accommodated. Across a range of natural mortality (M) scenarios (0.375-1.2??year-1), we determined the exploitation fraction (??) and fishing mortality (F) that protected 20% of the spawning potential of an unfished population, the current target. As M increased, ??20% and F-20% decreased. Assuming that M = 0.9??year-1, our models estimated ??20% = 0.45, which is greater than field-based estimates of ?? in 64% of the years since 1990. Hence, the commercial fishery has likely contributed to the recent population decline in Chesapeake Bay. Comparisons of our results with conventional per-recruit approaches indicated that incorporating the complexity of the fishery was the most important advantage in our individual-based modeling approach. ?? 2005 NRC.