Many asexual animal populations comprise a mixture of genetically different lineages, but to what degree this genetic diversity leads to ecological differences remains often unknown. Here, we test whether genetically different clonal lineages of Aptinothrips grass thrips differ in performance on a range of plants used as hosts in natural populations. We find a clear clone-by-plant species interactive effect on reproductive output, meaning that clonal lineages perform differently on different plant species and thus are characterized by disparate ecological niches. This implies that local clonal diversities can be driven and maintained by frequency-dependent selection and that resource heterogeneity can generate diverse clone assemblies.