Bryophytes are amongst the most ancestral terrestrial plants and often have large distribution ranges across continents. Recent biochemical and molecular studies have suggested that many worldwide morphological species of bryophyte may represent genetically divergent and reproductively isolated cryptic species. We tested the cryptic species hypothesis in the thalloid liverwort Aneura pinguis complex. We applied analyses of chloroplast DNA (cpDNA) sequence variation and polymerase chain reaction‐restriction fragment length polymorphism (PCR‐RFLP) methods to discriminate between specimens of A. pinguis derived from various habitats in five distant geographical regions in Poland. Of the 19 specimens sequence characterized for the cpDNA tRNALeu region, seven haplotypes were identified divided into three nonmonophyletic clusters. The application of developed PCR‐RFLP markers confirmed the existence of three tRNALeu types of A. pinguis (A–C) within the specimens derived from 21 populations. Sympatric populations of different tRNALeu types were found in lowland and mountain regions. No clear correlation between stand type and the presence of two tRNALeu types (A, B) was observed, as both were growing on soil, humus, and rocks. The tRNALeu type C was found only on humus and its distribution was restricted to low‐lying northern populations. The above results indicate that the A. pinguis complex is highly differentiated at the molecular level and may represent three cryptic species. © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society, 2007, 155, 273–282.