The polychaete Capitella capitata is historically one of the most commonly used indicators of organic enrichment in marine benthic environments. However, this taxon has been used to refer to several cryptic species with distinct environmental tolerances, which may compromise ecological assessment and monitoring programs. In this study, we aimed to (1) assess the overlap and patterns of dominance in the spatial and temporal distribution and response to environmental variability of different species of the C. capitata complex in an urbanized coastal area and (2) investigate how the taxonomic resolution (species vs genera) could affect the observed patterns (i.e., whether the acknowledgement of cryptic species may affect the outcome of ecological assessments). Eight sampling campaigns were carried out from September 2011 to September 2013 in a heavily anthropized tidal flat in Southeastern Brazil. Four species of the complex were identified. Capitella nonatoi was the most abundant (~80% of the total abundance). Overall, the four species of Capitella showed high overlap in spatial distribution, especially between the most abundant ones. At community level, taxonomic resolution did not influence the perceived relationships with environmental and spatial variables, a result likely driven by the dominance of C. nonatoi and relatively high spatial overlap among species. The assemblage was influenced mainly by chlorophyll a and hydrocarbons, corroborating the indicator status of the taxa. At species level, however, individual response to environmental variability differed, suggesting that species may have distinct requirements. Thus, the use of a particular taxonomic resolution in ecological studies depends on the questions to be addressed. The recognition of cryptic diversity may be important for biodiversity assessments and studies at the population level (i.e., dynamics, behavior). Although further studies are needed to corroborate the observed patterns of dominance at larger scales, for community-level assessments, our results suggest that identifying Capitella to species level may not be needed for local ecological monitoring.