Shoot productivity and overwintering survival of gentians (Gentiana sp.) are determined by the initiation and subsequent development of crown bud clusters. Understanding of the anatomical features and origins of crown buds and bud clusters, and plant ontogeny, the morphological features of crown buds, and their associated development is required to achieve manipulation of bud initiation, emergence, and development. Anatomical features of the crown bud clusters were examined using both light and confocal microscopy using hybrids of Gentiana triflora × G. scabra. The initiation of bud clusters presented characteristics typical of adventitious buds in terms of their origin and presence of external vascular connection to the parental tissue. In contrast, crown buds forming subsequently within the cluster developed as axillary buds within that initial bud, collectively forming on a compact stem with minimal internode elongation. Stem elongation within the cluster after application of gibberellic acid enabled identification of a hierarchical arrangement of buds within the cluster with one bud at each node and arranged spirally at 90°. Arrangements of buds within the cluster were different from the opposite decussate phyllotaxis in floral shoots with two axillary buds at each node. Based on the current study, a crown bud cluster originated from a first bud initial, which was adventitious followed by development of subsequent crown buds within the cluster as axillary buds from this first bud initially with a single bud developing at each node.