This paper investigates urban imaginaries conveyed in publications in ecology over the past century. We examine some urban ecologists’ view that urban areas have been disregarded by ecology due to negative views on cities and urbanisation. Inspired by previous work on imaginaries in social and cultural geography and political ecology, and by textual data analysis methods, we adopted a methodological framework that applies both quantitative and qualitative methods in the analysis of a corpus of 960 articles (published 1922–2018) drawn from 10 long-standing international journals in ecology. Our hypothesis is that ecology has embraced an anti-urban imaginary that is manifested in urban invisibility as well as the recurrent expression of negative ideas about cities (constituting an ‘anti-urban bias’). Our results partially confirm this hypothesis. We show that until the 1970s only a few papers were published on cities. We identify nine main themes relating to cities around which ideas about cities have been constructed (threats, pests, refuges, fragmentation, gradients, pollution, homogenisation, planetary urbanisation, and planning) and show how these ideas have been mobilised in the articles since the 1920s. We discuss the way in which these evolving ideas reflect a move from an essentially anti-urban imaginary to a more complex and ambivalent one. This shift coincides with the rise of the idea of planetary urbanisation in ecological publications, increasing recommendations regarding urban planning, and more generally, growing conceptual debates on the ecological impact of cities.