In times of rapidly increasing multiple anthropogenic impacts on polar marine ecosystems and biodiversity, understanding, sustainable-use management and protection of these biotas is a matter of great concern. Research on marine biotas and their interactions with each other and the environment is fundamental in that regard, but available data are still diverse and scattered, as they exist in many formats and sources, such as published literature, data repositories, and unpublished material. Due to this heterogeneity, information is difficult to find, access and combine, severely impeding its reuse for further scientific analysis and its long-term availability for future generations. Scientists, decision makers, and the public require a versatile tool to compile, synthesize and manage biodiversity data in a transparent, efficient and comprehensible way and with high-level quality assurance. To address this challenge, we developed, implemented and utilize CRITTERBASE (https://critterbase.awi.de), a publicly accessible data warehouse and interactive portal that complies with the FAIR principles (Findability, Accessibility, Interoperability and Reusability of data). Its purpose is to complement long-term data storage repositories by providing powerful but easy-to-use data ingest, retrieval and exploration tools, thus facilitating the analysis of biodiversity data across multiple spatial and temporal scales and in wider contexts. Currently, it hosts quality-controlled and taxonomically standardized presence/absence, abundance, and biomass data from Arctic, North Sea and Antarctic regions, collated from the literature, unpublished data, own research and online repositories (with all metadata and links to primary sources included), for 3,173 polar benthic taxa (2,444 of which at species level) from 12,209 samples collected with grabs, underwater imaging or trawls between 1800 and 2014. CRITTERBASE is currently holding benthic biodiversity data only but because of its comprehensive and flexible data model it is suited to include information about further biotas and habitats. Therefore, we envision it becoming a valuable and continuously expanding tool for a wide range of usages, such as studies of spatio-temporal biodiversity patterns, impacts and risks of climate change or the evidence-based design of marine protection policies.