Flying-foxes (Pteropodidae) show a high rate of island endemism, but island-endemic taxa have shown a high rate of decline and extinction, mostly because their small population sizes are susceptible to hunting pressure and habitat loss. The Christmas Island flying-fox is restricted to the 135 Km² Christmas Island (Indian Ocean), as either an endemic species Pteropus natalis or a markedly distinct subspecies of Pteropus melanotus. Given recent declines and extinctions of other native vertebrate species on this Island, this study sought to monitor population trends for this taxon. Monitoring flying-foxes at roost sites is difficult because they are highly vagile, not all roost sites may be known to observers, and dense vegetation at some sites may make counts inaccurate. These constraints are particularly evident on Christmas Island. In this study, we sought to establish a monitoring program complementary to roost counts, and to assess changes in reporting rate from a baseline sampling of 107 sites spaced across the Island in 2006 to a repeat sampling of those sites in 2012. Every site was visited four times, at night, over a period of 4–6 weeks in June–July of 2006 and of 2012, and observers reported whether or not they heard or saw flying-foxes around the sample site. A reporting incidence measure (varying from 0 to 4) was derived for every site. This measure showed a significant decline (of 39%) between the 2006 and 2012 sampling. The observed rate of decline suggests that this taxon is of considerable conservation concern, and merits further conservation action: indeed in 2014 its Australian conservation status was changed from not listed to Critically Endangered. The cause of the current decline is not yet known, but this study indicates that factors additional to hunting and habitat loss may affect island flying-fox species.