The Endangered Madagascar giant jumping rat, Hypogeomys antimena, has suffered a major decline in distribution and is now restricted to two seemingly unconnected sub-populations in the largest remaining fragment of deciduous, seasonally dry forest in Menabe, western Madagascar. In a previous study a rapid decrease in numbers of H. antimena was observed in relatively intact forest, suggesting a factor of population decline additional to habitat loss, and provoking fears of a negative trend occurring across its remaining range. In the current study we conducted extensive line transect surveys to estimate active H. antimena burrow density in 2004 and 2005 as an index of population size, and trapping to estimate mean group size, as a multiplier for population size estimation. Within the surveyed areas we estimated the combined size of the two H. antimena sub-populations in 2005 to be c. 36,000, considerably larger than previously assumed. There was no evidence that active burrow density across the species’ known range changed between 2000 and 2005. H. antimena was not uniformly distributed, with higher densities of active burrows found in forest with the highest canopy in areas furthest from forest edges. These core forest areas are vital for the species’ conservation and the recent declaration that the Menabe forest will receive statutory protection provides hope that H. antimena may be safeguarded. However, given its restricted range and low reproductive output, among other factors, H. antimena remains threatened and requires close future monitoring.