This dataset is a component of the PAN-Arctic data collection of benthic BIOtas (PANABIO) and has been collated during the Census of Marine Life project Arctic Ocean Diversity (ArcOD; http://www.arcodiv.org/). It contains a total of 667 presence records of 244 megabenthic taxa (species to genus level) identified in 30 Agassiz trawl catches taken at 30 stations located in various Canadian Arctic seas at water depths of 38–759 m during two cruises in 2007 and 2008. The dataset is also available in a PostgreSQL-based data warehouse that can be accessed and queried through an open-access frontend web service at https://critterbase.awi.de/panabio.