The development of efficient sequencing techniques has resulted in large numbers of genomes being available for evolutionary studies. However, only one genome is available for all amphibians, that of Xenopus tropicalis, which is distantly related from the majority of frogs. More than 96% of frogs belong to the Neobatrachia and no genome exists for this group. This dearth of amphibian genomes greatly restricts genomic studies of amphibians and, more generally, our understanding of tetrapod genome evolution. To fill this gap, we provide the de novo genome of a Tibetan Plateau frog, Nanorana parkeri, and compare it to that of X. tropicalis and other vertebrates. This genome encodes more than 20,000 protein-coding genes, a number similar to that of Xenopus. Although the genome size of Nanorana is considerably larger than that of Xenopus (2.3 vs 1.5 Gb), most of the difference is due to the respective number of transposable elements in the two genomes. The two frogs exhibit considerable conserved whole-genome synteny despite having diverged about 266 Ma, indicating a slow rate of DNA structural evolution in anurans. Multi-genome synteny blocks further show that amphibians have fewer inter-chromosomal rearrangements than mammals but have a comparable rate of intra-chromosomal rearrangements.With the new genome used as reference, multi-tissue transcriptomes of five Nanorana species with much different habitat altitudes were further generated, and genes underlying the N. parkeri's adaptations to extreme environments were identified with comparative analysis methods. The new genome offers an improved understanding of evolution of tetrapod genomes, and also provides a genomic reference for other evolutionary studies.