Talpidae includes 54 recognized species distributed in Eurasia and North America. Talpids are characterized by diverse ecomorphologies, and are promising taxa to examine adaptive evolution. Surprisingly, no transcriptome data has been collected ever for any species of this family. In this study, we sequenced the transcriptomes of the heart and lung of Uropsilus gracilis and spleen and lung of Euroscaptor kuznetsovi. U. gracilis is a terrestrial species representing a relict group endemic in southwestern China and adjacent Northern Myanmar, and E. kuznetsovi is a fully fossorial species of the tribe Talpini. The distribution of E. kuznetsovi in China is also reported here for the first time. By de novo assembling, we obtained 197 092 and 225 956 transcripts of U. gracilis and E. kuznetsovi, respectively, and 12 5427 and 94 023 unigene correspondingly. By comparison with data from genome annotation data from GenBank, we revealed 8 376 orthologous genes among three talpid species and 8 114 orthologs among talpid and shrew species. We found more than 10 tissue-specific genes in the highly expressed genes for each tissue. On the other hand, BUSCO analysis suggested that single-copy genes were 43.0% and 56.6% complete in U. gracilis and E. kuznetsovi, respectively, suggesting that the mRNA rapidly degraded after the death of the animals, and hindered the assembly of the transcriptomes. We revealed that 335 genes were highly expressed in the lung of E. kuznetsovi, including HMGB1, HSPD1, SF3B1, COL3A1, SUMO1 and JUNB by comparing the expression differences of lung genes between the two species, These genes were reported to be related with hypoxia or high-altitude adaptation.