The endangered minnow Iberochondrostoma almacai is an endemic Iberian cyprinid with a restricted and fragmented distribution. Here, we describe the genetic structure of the species and infer its demographic history from six nuclear-encoded microsatellite loci and mitochondrial cytochrome b sequences. Genetic diversity was low (microsatellite He<0.45; mtDNA π<0.0015), and both markers resolved two groups: one from the northern Mira drainage and one from the Arade and Bensafrim drainages. The relatively low differentiation between these groups (0.09<FST<0.29; 0.31< ΦST <0.57) suggests past headwater captures and/or that populations were large until recently. The genetic diversity and differentiation estimates were compared with those for other three endangered cyprinids inhabiting similar intermittent rivers. Microsatellite data indicate a population decrease in the last 100–2400 years, probably as a result of anthropogenic disturbance. Human activities together with an intermittent flow of these rivers apparently led to local extinctions with consequent fragmentation and contraction in range. We recognize two management units corresponding to the two genetic groups identified. To maintain/increase genetic diversity, we recommend habitat restoration actions and measures to increase gene flow within and/or between the two units, under controlled reproductive programmes. Ecological experiments should be performed to ensure the success of supplementation among the two units. Moreover, the reintroductions in unoccupied drainages are suggested if further data confirm the presence of I. almacai in the recent past.