The Malayan pangolin (Manis javanica), an unusual mammal that is a scale-covered, toothless specialist myrmecophage, is maintained primarily through captive breeding in China.  Maintaining this species in captivity is a significant challenge partly because little is known about its behavior and reproduction. The molecular mechanisms of its digestive system play a key role in the feeding and dietary husbandry of pangolins in captivity. Here, we performed the first large-scale sequencing of M. javanica transcriptomes from three digestive organs—the salivary glands, liver and small intestine—by using Illumina HiSeq technology to provide useful genetic resources for future functional work that may be relevant for the maintenance of captive pangolins.