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Plant growth in a controlled environment system is highly dependent on the availability of light. The light-emitting diode (LED) is capable of providing the needed quality and quantity of light for the plant. The purpose of this study was to determine the effect of white LED light intensity on the growth of in vitro propagated apple (M-9) seedlings in a controlled environment system. Seedlings were grown for 30 days under five different white LED light intensities: 100–500 (L1), 250–500 (L2), 500–500 (L3), 250–250 (L4), and 100–100 (L5). Our findings indicate that seedlings treated with L3 grew substantially taller than seedlings treated with L1, L2, or L5. The number of leaves, stem diameter, shoot fresh weight, root fresh weight, and shoot dry weight of L3 treated seedlings were considerably greater than those growing in other treatments. Furthermore, root length, root dry weight, chlorophyll content, and photosynthesis rate were considerably increased in the L3 treatment group compared to the L5 treatment group. However, there was no significant difference in the stomatal conductance or transpiration rate of apple seedlings between the light treatments. Moreover, a positive correlation was seen between stomatal conductance and transpiration rate. These results suggest that light intensity PPFD 500-500 were favorable for the initial growth of in vitro propagated apple seedlings.