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Populations that experience human\u2010induced range reductions are often highly inbred and lack genetic diversity, but it is unknown whether this is also the case for populations with naturally small ranges. The fishes <jats:italic>Poecilia sulphuraria<\/jats:italic> (listed as critically endangered) and <jats:italic>Poecilia thermalis<\/jats:italic>, which are endemic to small hydrogen sulphide\u2010rich springs in southern Mexico, are examples of such populations with inherently small habitats. We used geometric morphometrics and population genetics to quantify phenotypic and genetic variation within and among two populations of <jats:italic>P.\u00a0sulphuraria<\/jats:italic> and one population of <jats:italic>P.\u00a0thermalis<\/jats:italic>. Principal component analyses revealed phenotypic and genetic differences among the populations. Evidence for inbreeding was low compared to populations that have undergone habitat reduction. 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