The octopus fishery in the state of Yucatan is one of the most important in Mexico and landings have doubled over the past decade causing an increase in the demand for crabs used as bait. Data on bait composition and their harvest are limited even though its economic and ecological impact could be considerable. DNA barcoding of the 16S gene was used to identify the species of crustaceans in 93 samples of bait collected from 12 localities from Yucatan during August to October 2022. A total of nine species of crustaceans were identified, from which the mangrove crab Ucides cordatus was the most frequent (61%), followed by the longnose spider crab (Libinia dubia, 14%), and the Caribbean spiny lobster (Panulirus argus, 8%). The use of bait shows strong spatial patterns, including the local exploitation of some species and the import of bait from various geographical sources from other adjacent Mexican states to meet the demand. Although some sustainable practices were documented, such as using the discarded cephalotorax from the fishery of Caribbean spiny lobster, at least one species banned as bait by fisheries regulations (the stone crab Menippe mercenaria) was also identified. The American horseshoe crab (Limulus polyphemus), a protected species of national and international conservation concern, was absent in this samples. This study suggests that bait harvest for the octopus fishery could potentially impact both local and distant crab populations, and highlights the need to create and improve existing regulations for bait harvest that need to be built and clearly communicated within the fishing communities to improve the sustainability of the fishery.