Promoters of urban ecology commonly point to the historical absence of the city in ecology. This assertion is obviously meant to highlight the novelty and timeliness of urban ecology and to plead for its development. Given the founding role of this ignorance narrative for urban ecology, we deemed it essential to explore whether and how it could be empirically substantiated. Drawing on ignorance studies, we propose to investigate knowledge blind spots and questions left uncharted by the dominant research agendas in ecology. Stepping aside from the shared assumptions within the urban ecology community, we set up to explore the main features of a regime of (im)perceptibility of the city in ecology. To this end, and using a mix of methods including bibliometric and textual data analyses, observations and interviews, we combined the exploration of global scientific publications, naturalist inventories in Swiss research institutions and cities and everyday ecological research practices in Switzerland. Our analysis leads to nuancing the binary representation of the city as either absent or present in ecological research. It highlights three dimensions (epistemic framings, field practices and institutional marginality) that may explain the imperceptibility of the city in ecological research. We demonstrate the existence of ecological research in the city before and alongside self-declared ‘urban ecology’. Ignorance studies generally aim to expose biased historiographies and address the politics of contentious knowledge. We hypothesize and show that this analytical framing can also shed light on the obfuscation of past and rival research in the formation and consolidation of epistemic communities.