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Overfishing of sea cucumber <i>Isostichopus badionotus</i> from Yucatan has led to a major population decline. They are being captured as an alternative to traditional species despite a paucity of information about their health-promoting properties. The transcriptome of the body wall of wild and farmed <i>I. badionotus</i> has now been studied for the first time by an RNA-Seq approach. The functional profile of wild <i>I. badionotus</i> was comparable with data in the literature for other regularly captured species. In contrast, the metabolism of first generation farmed <i>I. badionotus</i> was impaired. This had multiple possible causes including a sub-optimal growth environment and impaired nutrient utilization. Several key metabolic pathways that are important in effective handling and accretion of nutrients and energy, or clearance of harmful cellular metabolites, were disrupted or dysregulated. For instance, collagen mRNAs were greatly reduced and deposition of collagen proteins impaired. Wild <i>I. badionotus</i> is, therefore, a suitable alternative to other widely used species but, at present, the potential of farmed <i>I. badionotus</i> is unclear. The environmental or nutritional factors responsible for their impaired function in culture remain unknown, but the present data gives useful pointers to the underlying problems associated with their aquaculture.