The aim of this study was to determine the morphological and genetic variability of four Nepeta genotypes: N. cataria var. citriodora, N. × faassenii, N. mussinii, and N. nuda from the Collection of Medical Plants in Dołuje, Vegetable Faculty, Agricultural University of Szczecin, Poland. Morphological variation among the examined catnip forms was determined using biometric measurements which included the plants height, the width of a leaf pair, the length and width of a leaf blade, the length of an inflorescence, the weights of fresh and dried green parts and the essential oils content. The DNA polymorphism within microsatellite sequences was determined using the ISSR-PCR technique. The conducted biometric measurements proved that the examined Nepeta plants differed significantly in all analysed features. Twenty microsatellite primers were used in ISSR reactions; clear products were generated in reactions with six of them. In general, 72 loci were amplified (110 amplicons); five of them (7%) turned out to be monomorphic, 20 (28%) polymorphic and 47 (65%) were specific for the examined accessions. Unique loci were amplified for each examined Nepeta genotype. A phylogenetic tree was constructed on the basis of a UPGMA cluster algorithm. It consisted of one similarity group ‘a’, in which N. × faassenii, N. mussinii and N. nuda were included.