Classical approaches to fisheries stock assessment and thus management rely on methods that are expensive, time-consuming, and not conducive to managing data poor stocks. Moreover, many nearshore rocky reef species exhibit spatial variation in harvest pressure and demographic rates that further limiting traditional approaches to stock assessment. In response to these management challenges, ecologists from the SBC LTER began working with local spiny lobster and rockfish fishermen, resource managers, and NGO scientists to overcome data limitations and develop spatial-based approaches for fishery management. The key partnership (CALobster: www.calobster.org) is a cooperative relationship between fishermen and SBC LTER scientists, in which fishermen teach scientists fishing techniques, history, culture, and “local ecological knowledge” which scientist incorporate into their methods of stock assessment. In return, scientists teach fishermen hypotheses formation, experimental design, rigorous sampling protocols, statistical analyses, and data reporting, which they use to help improve management of the fishery. This unique collaboration between scientists and fishermen extends to publishing peer-reviewed papers together. In doing so, former adversaries in ecosystem conservation and management have become partners that have generated new ideas, methods, and data for collaborative, spatial-based fishery management in the Santa Barbara Channel. With the recent implementation of local no-take Marine Reserves in the Santa Barbara Channel, SBC LTER’s research collaboration has focused on identifying and measuring how reserves function as fishery management tools in three principal areas: (1) through the provision of ecological baselines used to gauge the impact of fishing on populations of target species and associated communities, (2) as refuges that serve as a source of adults, juveniles, and larvae that spillover from reserves to adjacent fished areas; and (3) by altering the spatial distribution of fishing effort, yield, and revenue. Together we have measured natural and fishing mortality of lobster and rockfish, information that is being used to enhance traditional stock assessments, as well as establish collaborative, small-scale, and more cost-effective management approaches, such as a Decision-tree framework for setting annual grass rockfish harvest quotas. A novel finding that has come about through the synthesis of SBC LTER time series data on kelp forest community dynamics, lobster fishery data, and interviews with fishermen is that, in contrast to previous reports, lobster fishing per se probably does not lead to a trophic cascade in California’s kelp forests in which decreases in lobster, lead to increases in sea urchins, which in turn reduce the abundance of giant kelp.