We analyze the long term behavior of interacting populations which can be controlled through harvesting. The dynamics is assumed to be discrete in time and stochastic due to the effect of environmental fluctuations. We present extinction and coexistence criteria when there are one or two interacting species. We then use these tools in order to see when harvesting leads to extinction or persistence of species, as well as what the optimal harvesting strategies, which maximize the expected long term yield, look like. For single species systems, we show under certain conditions that the optimal harvesting strategy is of bang-bang type: there is a threshold under which there is no harvesting, while everything above this threshold gets harvested. The second part of the paper is concerned with the analysis of ecosystems that have two interacting species which can be harvested. In particular, we carefully study predator-prey and competitive Ricker models when there are two species. In this setting we show how to find the optimal proportional harvesting strategy. If the system is of predator-prey type the optimal proportional harvesting strategy is, depending on the interaction parameters and the price of predators relative to prey, either to harvest the predator to extinction and maximize the asymptotic yield of the prey or to not harvest the prey and to maximize the asymptotic harvesting yield of the predators. If the system is competitive, in certain instances it is optimal to drive one species extinct and to harvest the other one. In other cases it is best to let the two species coexist and harvest both species while maintaining coexistence. In the setting of the competitive Ricker model we show that if one competitor is dominant and pushes the other species to extinction, the harvesting of the dominant species can lead to coexistence.