Studying offshore natural and artificial hard substrates in the southern North Sea (51ºN–57ºN/1ºW–9ºE), the invasive introduced Japanese skeleton shrimp Caprella mutica Schurin, 1935 was found to co-exist with the native Caprella linearis (Linnaeus, 1767) only on near-shore locations that had an intertidal zone (e.g., wind farm foundations). In contrast, on far offshore and strictly subtidal locations, such as shipwrecks and rocky reefs, only C. linearis was found. Based on these exploratory observations, we hypothesised that artificial structures that are only subtidal are inhabited exclusively by C. linearis, and never by C. mutica. To test this hypothesis and understand factors driving each species’ habitat preferences, habitat suitability models were constructed using generalised additive models, based on samples collected in 2013–2015 from offshore gas platforms, buoys, shipwrecks, and rocky reefs and combined with data from other published and unpublished surveys (2001–2014). The models showed that the presence of C. mutica is explained by the availability of intertidal and floating hard substrates, suspended particulate matter density (SPM), mean annual sea surface temperature, salinity, and current velocity. The C. linearis model included subtidal hard substrates, SPM, salinity, temperature, and current velocity. The modelled distributions showed a significant difference, demonstrating that C. linearis’ habitat preference does not fully overlap with that of C. mutica. Thus, the native and alien Caprella species are likely to be able to co-exist in the North Sea.