Genetic relationships of black-fruit hawthorns of the Carpathian basin have been investigated based on intergenic cpDNA sequences; first of all of the endemic Crataegus nigra and related species. Considerable infraspecific variation was detected in the East Asian taxon C. chlorosarca and some divergence in the Eurasian C. pentagyna. Based on the genetic analysis of investigated and reference psbA-trnH sequences, classification of sections Crataegus and Sanguineae is highly supported. From the studied taxa, C. pentagyna and C. monogyna was ordered to Sectio Crataegus, while C. nigra and .C. chlorosarca to Sectio Sanguineae. Based on our data, C. nigra can be considered as maternal parent of the investigated C. × degenii hybrids.