In Mexico, as in other parts of the world, there is limited knowledge regarding the operation of small-scale fisheries. Also, there is an urgent need for the diversity of fisheries and their interactions, and the diversity of species to be analyzed on a regional level. In this study, the dynamics of the small-scale fleet operating in San Ignacio in the northwestern Pacific of the state of Baja California Sur were analyzed, recognizing the fishery’s multi-species and multi-gear character and its effect on the spatial and temporal distribution of the fishing effort. The operative units (OU) approach was applied; OUs are defined as the set of associated vessels that exploit one or more target species using similar fishing gears. The information about species, gears, sites and fishing seasons was obtained from interviews with 74 fishers. The OUs identified included: diving-pen shell scallop; diving-squalid callista; diving-Pismo clam; collection-black ark; trap-barred sand bass; trap-crab; trap-lobster; cast net-shrimp; bottom net-fish; surface net-fish; bottom net-shark. The variation in the activity of each OU is related to the availability of the resources, prices of the products and official restrictions. From a management perspective, this method helps to clarify which OUs adhere to specific rules associated with their métier and others, which are less well defined since their OU characteristics are associated with their fishery level. The definition and characterization of the OU, based on the local knowledge of the fishermen, assist the design of management schemes that consider the spatial and temporal complexity of the small-scale fisheries.