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Predicting future conservation needs can help inform conservation management but is subject to uncertainty. We measured deforestation rates during 2015–2017 for 114 protected areas in Madagascar, linked deforestation to the status of protection according to IUCN categories I–VI, used recent deforestation rates to extrapolate forest cover over 2017–2050 and linked the size of forest blocks to the projected persistence of lemur subpopulations. In the six IUCN categories for protected areas in Madagascar the median size of forest blocks is 9–37 km2 and median annual deforestation rates range from 0.02% in the single IUCN category III site to 0.19% in category II and 1.95% in category VI sites. In 2017, 40% of all forest blocks within protected areas were < 10 km2, and this is projected to increase to 45% in 2050. Apart from these small forest fragments, the modal site of forest blocks was 160–320 km2 in 2017, and this is projected to decrease to 80–160 km2 in 2050. The range of > 50% of all lemur species exclusively contains forest blocks of < 10 km2. The modal size of forest blocks > 10 km2 is predicted to remain at 120 km2 until 2050. Although uncertainty remains, these analyses provide hope that forest blocks within the protected areas of Madagascar will remain large enough to maintain lemur subpopulations for most species until 2050. This should allow sufficient time for the implementation of effective conservation measures. [ABSTRACT FROM AUTHOR]