Indonesian tuna fisheries are complex due to variation in the scale of fleet in the fisheries, their multi-species nature and problems with data collection. Moreover, like many developing-country fisheries, their management needs to take into account many other goals besides rents maximization, such as the distribution of rents and the stability of income and employment. This study evaluate the performance of alternative management procedures by means of a stochastic bio-economic model integrating the characteristics of three different scales of fishing, two tuna species, and partly unobserved catch. We focus on skipjack and yellowfin tuna fisheries in the eastern Indonesia in small-scale fleet, medium-scale fleet, and large-scale fleet of tuna fisheries. We combine the dynamics of an age-structured production model and the economic performance of fishing activity. We use reference points of catch per unit effort (CPUE) as representative of relative abundance to update the total number of allowable fishing effort next year. We discuss the performance of the management procedures with respect to aggregate rents, distribution of rents, and stability of fishing effort.