Phenotypic polymorphism represents the most obvious type of intraspecific diversity raising scientific interest in its evolution and maintenance. We studied the regional endemic Gentianella bohemica, which exhibits an early- and a late-flowering morph. Genetic variation and structuring were investigated in relation to potential pollination and mating system differences, to verify hypotheses of evolutionary integrity, origin, and reproductive isolation of both flowering morphs. We identified the rarer early-flowering morph as an independent genetic entity, being more selfing, likely stronger pollinator-limited and reproductively isolated. All analysed populations showed strong among population differentiation and low overall genetic diversity due to habitat fragmentation and reduced population sizes. These results indicate likely inbreeding, but we also found evidence for possible outbreeding depression in the late-flowering morph. Both G. bohemica morphs are characteristic of traditionally used, nutrient-poor grasslands, but they represent independent conservation units and need temporally adapted management. We, therefore, also briefly discuss our results in the general context of conservation activities in relation to intraspecific polymorphisms and strongly argue for their formal and consequent consideration.