Ex vitro rooting and acclimatization of two cultivars ‘Wojtek’ and ‘Zojka’ of blue honeysuckle (Lonicera caerulea var. kamtschatica Sevast.) were studied. To the ex vitro conditions were transferred rooted and unrooted shoots. The post-effect of auxin type and concentration as well as microcutting and soil substrate types were tested. The genetic stability of the plantlets in relation to the mother plants by using amplified fragment length polymorphism (AFLP) and inter simple sequence repeat (ISSR) markers has been also determined. It has been found that in vitro rooted cuttings of both cultivars showed a higher survival rate (max. 88%) and better growth and development when they were rooted on a medium containing a low auxin level (1.0 mg·dm−3). The results of the second experiment showed successful ex vitro rooting of blue honeysuckle shoots without auxin treatment. Higher ex vitro rooting and survival rate in the greenhouse have been observed for ‘Wojtek’ (max. 96%) than ‘Zojka’ (max. 88%). Better growth and development of shoots and roots were observed on peat alone or a mixture of peat and perlite as compared to a mixture of peat and sand. The micropropagated plantlets appeared similar to mother plants. Molecular analysis confirmed a high level of genetic stability of blue honeysuckle after 2 years of in vitro propagation. However, among the cultivars studied, ‘Wojtek’ showed slightly higher genetic stability than ‘Zojka’ (99.5% and 97.7%, respectively). For ‘Zojka’ plants, the degree of variation was comparable for AFLP and ISSR markers. For ‘Wojtek’, no polymorphism was detected using the ISSR analysis in contrast to the AFLP analysis.
