To compare the effect of 6-benzylaminopurine (BAP) and thidiazuron (TDZ) on morphological abnormal plants or per cent variant plantlets during secondary hardening period. Shoot tips of Musa spp. were cultured on MS medium supplemented with different concentrations (2.0 and 5.0 mg/L) of BAP and (0.2 and 0.3 mg/L) of TDZ and NAA 0.2 mg/L. Wherever, TDZ is present in the medium some morphological dwarf plants were observed. The maximum plant height (16.17 cm) and number of leaves (4.20) was in T 2 . Where, the maximum shoot diameter (4.97 mm), number of primary roots (4.53) and length of longest root (11.17 cm) was in T 1 . TDZ at 0.2 mg/L it increases the morphological abnormal plants like dwarf plants (20.00%). In conclusion BAP at 5.0 mg/L, TDZ at 0.2 mg/L and NAA at 0.2 mg/L and BAP at 2.0 mg/L, TDZ at 0.2 mg/L and NAA at 0.2 mg/L were assumed to be the most suitable for commercial micropropagation system with low frequency of abnormal shoot production for local banana cultivars. Highlights •BAP is the best for healthy, thinner and lengthy shoots.• Dwarfness is the major abnormality during hardening where ever TDZ is used.• Rooting (90-95%) was successfully obtained in NAA medium and survival of plantlets (70-75%) during hardening.

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