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PremiseCommon taxonomic practices, which condition species' descriptions on diagnostic morphological traits, may systematically lump outcrossing species and unduly split selfing species. Specifically, higher effective population sizes and genetic diversity of obligate outcrossers are expected to result less reliable phenotypic diagnoses. Wild tomatoes, members ofSolanumsect.Lycopersicum, are commonly used as a source of exotic germplasm for improvement of the cultivated tomato, and are increasingly employed in basic research. Although the section experienced significant early work, which continues presently, the taxonomic status of many wild species has undergone a number of significant revisions and remains uncertain. Species in this section vary in their breeding systems, notably the expression of self‐incompatibility, which determines individual propensity for outcrossing MethodsHere, we examine the taxonomic status of obligately outcrossing Chilean wild tomato (Solanum chilense) using reduced‐representation sequencing (RAD‐seq), a range of phylogenetic and population genetic analyses, as well as analyses of crossing and morphological data. ResultsOverall, each of our analyses provides a considerable weight of evidence that the Pacific coastal populations and Andean inland populations of the currently describedSolanum chilenserepresent separately evolving populations, and conceal at least one undescribed cryptic species. ConclusionsDespite its vast economic importance,Solanumsect.Lycopersiconstill exhibits considerable taxonomic instability. A pattern of under‐recognition of outcrossing species may be common, not only in tomatoes, but across flowering plants. We discuss the possible causes and implications of this observation, with a focus on macroevolutionary inference.