Excelsa coffee (Coffea excelsa A. Chev.) species is known to be hard-to-root when propagated through stem cuttings. This study sought to examine the morpho-anatomical differences between Excelsa and Robusta coffee stem cuttings in order to identify any physical hindrances to rooting and to trace the origin of adventitious rooting in Excelsa coffee. Rooting of single-node orthotropic Excelsa coffee stem cuttings from water sprouts with and without incisions in the rooting zone applied with auxin plus ferulic acid takes 5 and 7 mo under mist, respectively. Morpho-anatomical examinations revealed that Excelsa coffee had thicker stem structures compared to Robusta coffee. However, the most probable anatomical difference why Excelsa coffee is harder to root when compared to Robusta coffee is its narrow, compact and clustered nearly continuous layer of sclerenchyma band as opposed to the discontinuous layer in Robusta coffee. The layer of sclerenchyma physically prevented root initial development which resulted in delayed rooting in Excelsa; this was observed to occur after 4 – 7 mo compared to Robusta coffee where rooting occurred within 1 – 2 mo. Restriction of rooting was a result of the physical hindrance on root initial development by the continuous sclerenchyma band rather than by preventing root protrusion or outgrowth. Basal incisions made in the rooting zone physically disrupted the layer of sclerenchyma that enabled the development of root initials which promoted more adventitious roots in the stem cuttings.