In marine benthic environments, oxygen availability is highly variable across temporal and spatial scales. Such variability generates heterogeneous microhabitats in which organisms experience marked changes from saturated (i.e. normoxic) to anoxic conditions. For sessile colonial species, fine spatial differences in oxygen availability can trigger intra-colony phenotypic differences, influencing the overall colony performance/fitness. Here, we assessed the extent to which intra-colony differences in oxygen regimens influence biological characteristics in adult and larval stages of the colonial bryozoan . For this, we measured the critical sensitivity to low oxygen for upper and lower zones of adult colonies and their larvae. We also measured larval swimming-exploring behaviour and settlement under hypoxia and normoxia. Although the results show similar intra-colony tolerances in the adults, differences were found in their larvae. While the lower zones of the colonies showed higher tolerant larvae, the upper zones had larvae with higher sensitivity and a tendency to avoid low-oxygen microhabitats. These larvae settle more quickly and in greater numbers compared with their lower-zone counterparts. Our results suggest that intra-colony differences in sensitivity to low-oxygen conditions (particularly during larval stages) can be important regulators of ecological processes (e.g. recruitment) and the resilience of benthic colonial species in deoxygenated oceans.