Mesotriton alpestris lacusnigri is regarded as being an extinct subspecies of the Alpine newt endemic to a small fishless alpine lake called Črno jezero (Black Lake) in the Julian Alps in Slovenia. To re-assess its taxonomic position we sequenced fragments of two mitochondrial genes (309 bp of cytochrome b and 315 bp of 16S rRNA) of two museum specimens collected in 1953. Specimens of the ssp. lacusnigri yielded two new haplotypes which formed a monophyletic group within a cluster of other Slovenian and central European haplotypes of ssp. alpestis. The name lacusnigri is therefore merely a junior synonym of the nominotypical subspecies and should be removed from red data listing. Our study highlights the outstanding value of natural history collections as baselines for contemporary biodiversity assessments.