Aim. 5S rDNA belongs to the moderately repeated, tandemly arranged sequences composed of coding regions and intergenic spacers (IGS). The IGS comparison is successfully used for the study of microevolution and in the molecular taxonomy of plants, vertebrates and some invertebrates. However, 5S rDNA of insects still remains insufficiently characterized. In this article, we analyze the molecular organization and polymorphism of 5S rDNA IGS of Apis mellifera ligustica. Methods. DNA extraction, PCR amplification, cloning of 5S rDNA, sequencing, bioinformatics analysis. Results. The 5S rDNA IGS of A. m. ligustica was cloned into the plasmid vector and sequenced. The obtained sequences were compared with the same genomic region of A. m. carnica. It was found that the genome of A. m. ligustica contains one class of IGS, which is represented by structural subclasses 1A, 1B, 1G and 1F. Two of these subclasses, 1G and 1F, which are identified here for the first time, are specific for A. m. ligustica. Conclusions. The obtained results show a high intra- and intergenomic polymorphism of 5S rDNA within the subspecies of Apis mellifera.Keywords: 5S rDNA, intergenic spacer, repeated sequences, Apis mellifera, Apidae.