Shedding light on the distribution and ecosystem function of mesopelagic communities in the twilight zone (~200-1000 m depth) of global oceans can bridge the gap in estimates of species biomass, trophic linkages, and carbon sequestration role. Ocean basin-scale bioacoustic data from ships of opportunity programs are increasingly improving this situation by providing spatio-temporal calibrated acoustic snapshots of mesopelagic communities that can mutually complement established global ecosystem, carbon, and biogeochemical models. This data descriptor provides an overview of such bioacoustic data from Australia's Integrated Marine Observing System (IMOS) Ships of Opportunity (SOOP) Bioacoustics sub-Facility. Until 30 September 2020, more than 600,000 km of data from 22 platforms were processed and made available to a publicly accessible Australian Ocean Data Network (AODN) Portal. Approximately 67% of total data holdings were collected by 13 commercial fishing vessels, fostering collaborations between researchers and ocean industry. IMOS Bioacoustics sub-Facility offers the prospect of acquiring new data, improved insights, and delving into new research challenges for investigating status and trend of mesopelagic ecosystems.