To obtain healthy and good quality plants from in vitro cultivation, it is necessary to produce plantlets with well-developed rooting systems because they must undergo acclimatization, a final and a very difficult stage of micropropagation. In the present research, the effect of auxins NAA, IAA and IBA in concentrations of 0.5; 1; 2.5 and 5 mg·dm−3 on the Paphiopediluminsigne in vitro rooting was studied, and it was noted that 1 mg·dm−3 of IAA or IBA enabled the obtaining of a lot of rooted and good quality plantlets. The subsequent influence of the two most advantageous auxins on the acclimatization of plantlets in different substrates (sphagnum moss, sphagnum moss + substrate for orchids, substrate for orchids, substrate for orchids + acid peat) was tested, in the means of morphological features of plants and their physiological parameters, i.e., chlorophyll fluorescence (FV, Fm, Fv/Fm), stress enzyme activity (catalase, ascorbate peroxidase), and water balance. Considering all the tested features, it might be stated that the best results were obtained when explants were rooted in vitro in the presence of 1 mg·dm−3 of IAA and then planted ex vitro in substrate for orchids.