The Montseny brook newt (Calotriton arnoldi) is a Critically Endangered amphibian species endemic to the Montseny Massif in Catalonia, Spain. Here we present a comparative genomics analysis of C. arnoldi and related salamander species, providing insights into the genomic basis of its adaptation to cold, fast-flowing mountain streams. We identify genes under positive selection related to osmoregulation and hypoxia response, and characterize the repetitive element landscape of the Montseny brook newt genome.