Common hyssop (Hyssopus officinalis L.) is widely used as an aromatic and medicinal plant. In the component composition of the essential oil from the above-ground mass of H. officinalis f. cyaneus, from the collection of the Nikita Botanical Garden, the bicyclic monoterpene ketones isopinocamphone (50.99–64.41%) and pinocamphone (3.95–18.88%) predominate, which allows us to attribute this form to the isopinocamphone chemotype for use in pharmacology. An essential oil sample with a high content of isopinocamphone (70.74%) in complete absence of pinocamphone was determined, which made it possible to use the plant as a starting material for breeding. The objective of our work was to study the component composition of the essential oil of this form, and the morphology, anatomy and ploidy level of microshoots in vitro on a nutrient medium with BAP. This was compared with ex situ samples to develop a cultivation technique with the preservation of a valuable trait for use in task-oriented selection. Biotechnological methods are used for future mass propagation, study and the preservation of breeding forms. Morphological and anatomical features and ploidy of H. officinalis microshoots were studied in vitro. Using in vitro culturing of microshoots on MS medium containing BAP, a decrease in the cuticular layer and the degree of development of collenchyma near vascular bundles in leaves were shown compared to microshoots ex situ. Significant structural changes were found with a high increase in BAP concentration, while no changes in the ploidy level were detected.