The Roach’s mouse-tailed dormouse (Myomimus roachi) is an endangered mammal in Europe with poorly known distribution and biology in Bulgaria. Cranial remains of 15 specimens were determined among 30532 mammals in Barn Owl (Tyto alba) pellets in 35 localities from 2000 to 2008 and 32941 mammals in Eagle Owl (Bubo bubo) pellets in 59 localities from 1988 to 2011 in SE Bulgaria. This dormouse was present with single specimens in 11 localities and whit 4 specimens in one locality. It is one of the rarest mammals in the region that forms only up to 1% by number of mammalian prey in the more numerous pellet samples. The existing protected areas ecological network covers six out of 15 (40%) localities where the species has been detected in the last two decades. We discuss the necessity of designation of new Natura 2000 zones for the protection of the Roach’s mouse-tailed dormouse in Bulgaria.