New pathologies are causing dramatic declines and extinctions of multiple amphibian species. In 2013, we found fire salamanders with undescribed cysts at the throat level in one population in Northern Italy, which existence is not reported in amphibians yet. With the aim of describing this novel phenomenon, we performed repeated surveys to assess the frequency of affected salamanders from 2014 to 2020, and integrated morphological, histological and molecular analyses. Cysts affected up to 22 % of salamanders of the study population and started spreading to nearby populations. Cysts are formed by mucus surrounding cells about 10 μm long, characterized by numerous undulipodia. Morphological and genetic analyses did not yield a clear match with any described organism or salamander cell. The occurrence of these cysts calls for more studies on the origin and impact on wild populations.