Explants of two elite cooking banana cultivars, FHIA17 and INJAGI were collected from healthy source of stock plants growing in the field. Sterilization was evaluated using different concentrations (20, 30, 40, 50 and 60%) of a commercial bleach (JIK) for 25 min. Effects of cytokinins benzyl amino purine (BAP), 2-isopentenyl adenine (2iP) and kinetin each evaluated at 5, 10, 20, 24 and 40 µM and thidiazuron (TDZ) at 0.1, 0.5, 1 and 1.5 µM, on microshoot induction were investigated. Effects of auxins viz. napthaleneacetic acid (NAA), indole-3-acetic acid (IAA), 2,4-dichlorophenoxyacetic acid (2,4-D) and indole-3-butyric acid (IBA each evaluated at 5, 10, 20 and 40 µM) on rooting were tested as well. The highest (91%) numbers of clean explants were obtained when the explants were subjected to sterilization in 40% Jik for 25 min. The FHIA 17 explants cultured on MS media supplemented with 40 µM kinetin produced the highest (3.00±0.35) mean number of microshoots. On the other hand, INJAGI explants cultured on MS media supplemented with 0.1 µM TDZ yielded the highest mean number (1.84±0.24) of microshoots and the highest mean length (0.99±0.13). Rooting was achieved in all media supplemented with the auxins evaluated except on 2,4-D. These results have an important significance on the application of tissue culture in propagation of cooking bananas in Rwanda, which is highly desired to support the government policy of replacing old unproductive bananas with elite high yielding varieties.