Populations in antagonistic coevolutionary interactions may "run or die," and their fates are determined by their evolutionary potential. The asymmetry of evolutionary speed between coevolving partners, for example, resulting from genetic constraints, can be mitigated in larger populations. We therefore hypothesize more frequent extinction driven by antagonistic coevolution with declining habitat size. In bacterium-virus systems, viruses (the consumers) typically suffer an evolutionary disadvantage due to constraints of genetic variation; and this pattern may apply to host-parasite interactions in general. Here, in our experiment with the bacterium Pseudomonas fluorescens SBW25 and its lytic phage virus SBW25Φ2, the likelihood of viral extinction was greater in smaller habitats. Among viral populations that did persist, those from small habitats showed lower infectivity and their coevolving bacterial populations had greater densities. Therefore, the impact of habitat size reduction on biodiversity could be exacerbated by coevolutionary processes. Our results also lead to a number of suggestions for biocontrol practices, particularly for evolutionary training of phages.