The Blue Chaffinch (Fringilla teydea) is endemic to the Canary Islands and restricted to the pine forests on Tenerife (ssp. teydea) and Gran Canaria (ssp. polatzeki). While the teydea population is large and stable, the polatzeki population underwent a dramatic decline in the twentieth century and currently numbers less than 200 individuals. Here, we show that microsatellite allelic diversity is lower in polatzeki than in teydea, consistent with a genetic bottleneck scenario. Our genotyped polatzeki individuals, which were wild-caught but currently used in a captive breeding programme, have the same allelic diversity as free-ranging birds. However, the captive polatzeki males seem to have reduced sperm motility as compared with captive teydea males, which could be an effect of reduced genetic diversity. Because polatzeki and teydea are phylogenetically distinct, they should be recognized as Evolutionarily Significant Units by conservation authorities. We also recommend maintaining the captive polatzeki population as a pre-emptive measure against extinction in the wild.