Toll-like receptors (TLRs) are an essential component of innate immunity. We report the first comprehensive assessment of TLR gene variation for urodele amphibians. The Lissotriton newt TLR repertoire includes representatives of 13 families and is compositionally most similar to that of the anuran Xenopus. Purifying selection has predominated the evolution of newt TLRs in both long and medium timescales. However, we infer that TLR genes undergo distinct trajectories of adaptive evolution in closely related newt lineages. This highlights the potential of TLRs to capture the signatures of different assemblages of pathogenic microorganisms, and suggests differences between lineages in the relative roles of innate and acquired immunity.