Marine reserves are proposed not only as a management strategy but also as a proxy for un-fished conditions. As fishing pressures have risen over time, scientists have had no way to control for fishing in populations being studied. With the help of models, we can begin to understand the effects of heavy fishing on populations by comparing them with “un-fished reserves” that are simulated by the model. I have done this using the species Mycteroperca microlepis (commonly known as gag) to build an explicit, individual-based model that looks at the effects of fishing on population dynamics. In order to better understand how to manage this species, I have created a model that has incorporated factors that have, up to now, been largely ignored: (1) explicit dispersal and connectivity between spawning grounds and seagrass nursery habitat, (2) pre- and post-dispersal density dependence, (3) stage-structured population, (4) spatially explicit and stage-specific movement, (5) stochastic population dynamics, and (6) the exploration of percent, placement, and size of marine reserves both by themselves and coupled with other management techniques. A sensitivity analysis on all parameters was performed using Latin Hypercube Sampling to determine which parameters had the greatest effect as well as which output variables were affected most. I found that (1) fishing exaggerated the skewed population demography of this protogynous hermaphrodite, (2) the effects of fishing had a much greater significant effect on effective population size than total population size, (3) sex ratio in the form of the fertility function did not have a significant effect on population demography, total, or effective population size, (4) spatial distribution has a significant effect, usually as an interaction, on effective population size therefore increasing its susceptibility to fishing pressure, (5) output variables were sensitive to life history aspects including natural mortality, sex change, fecundity, and recruitment, which were all highly correlated with multiple output variables, (6) effective population size was the most sensitive to change as compared to other output variables, and (7) size limit (where age limit was used as a proxy), reserves, and spatial variation in fishing were found to be effective management strategies when used both alone and in suites. This model can be used as a basis to be modified for other species in the Gulf of Mexico by changing life history methods. Overall, this model will be beneficial in better understanding the effect of fishing on the population structure and genetic viability of the population, and for predicting proper management strategies in a manner that is both habitat and species specific.