Ship rats (Rattus rattus) have successfully colonized six continents and 80% of islands worldwide by stowing-away on anthropogenic vessels. Numerous zooarchaeological and metagenomic studies have contributed to tracing the western dispersal of ship rats out of the Indian subcontinent and into the Mediterranean Basin, North Africa, and Europe. This has increased understanding of historical maritime mobility, trade contacts, and the spread of pandemic disease such as the plague. Moreover, considerable research has been conducted on the behavior, ecology, and population dynamics of ship rats in invaded areas, which supports conservation and eradication efforts. However, few studies have shed light on the mode of travel in between the geographic origins and destinations of ship rats, such as ships and boats, which act as mobile, commensal habitat for this cosmopolitan species. We address this lacuna here, by analyzing an assemblage of ship rat remains from an early Islamic period shipwreck, the Ma‘agan Mikhael B, located on the Carmel coast of modern Israel. Using zooarchaeological, biometrical, and palaeogenetic (aDNA) methodologies, we investigated the maritime ecology of ship rats regarding dispersal behavior, habitat selection, source–sink dynamics, and relative body size. The results of this study suggest that ship rats actively inhabited the Ma‘agan Mikhael B as part of their habitat selection processes, that conditions onboard provided high-quality habitat (adequate food and harborage, likely absence of predators and disease), and that they appear to have exhibited a degree of gigantism, possibly due to ‘island rule’. This study has implications for future metapopulation genetic studies on ship rats, as well as shows the value of zooarchaeological analysis in understanding the ecological circumstances of the maritime mobility of ship rats in the Mediterranean region.