The genus Ribes consists of several subgenera and approximately 150 species. Some authors divide the genus into two genera - currants and gooseberries. Within the genus, the level of hybridization is higher into gooseberries than in intersectional currants. Currant-gooseberry and intersectional hybrids were created artificially using polyploidy method. By morphological, palynomorphological, karyological and other characteristics, currant-gooseberry hybrids are contrasting. Tetraploid currant-gooseberry hybrids Josta and Kroma have pollen grains with an intermediate morphological type, and pollen of the triploid Dlinnokistnaya CGL is not typical for the family. We performed a comparative metagenomic analysis of these three hybrids of known origin and their parental forms (R. niveum, R. reclinatum, R. divaricatum and R. nigrum) in order to assess changes in their genomes for the ITS1 of 35S rRNA gene. Intragenomic polymorphism was studied by locus-specific NGS sequencing on the Illumina MiSeq platform using primers ITS-1P and ITS-2. It was shown that the ribotypes of the hybrids correspond to those of the parental forms. Ribotypes of unknown origin, highly homologous to other currants, were found. It has been shown that most of the pseudogenes are not conserved in hybrids. Comparative plant metagenomics is an informative method for studying hybridization and hybrids of unknown origin.