Abstract Background Eustoma grandiflorum is a new floral crop for the international flowers market, moderately cold-tolerant annual or biennial plant. A large number of seedlings can be produced by seed propagation but the quality is not uniform due to variations in the flowering time, plant height, and the number of flowers. Propagation of Eustoma grandiflorum plant by tissue culture technique is relatively low. Inducing mutations is one of the powerful tools for breeding biotechnology. Laser mutagenesis is an easy and new tool. The goal of the present work was to investigate the influence of laser irradiation on in vitro growth, anatomy, flowering, chemicals composition, and gene mutagenesis. Results The most of morphological, floral parameters, total chlorophyll, carotenoids, and anthocyanin pigment contents in the flower recorded increment by most treatments of laser types. The highest survival percentage of acclimatized plants (95%) and highest values of number of branches and branches length (cm) were obtained from treated plantlets by 20 min of green laser, while most of highest floral parameters, anthocyanin pigment contents in flower, and anatomical structural parameters recorded increasing using 20 min of blue laser and 20, 25 min of green and red laser, respectively. Contrary, the lowest values of photosynthetic pigments and carotenoids were obtained from 20 min of green laser. Conclusions The current research concluded that laser irradiation has remarkable effect on plant morphology, flowering, chemical constituents, and gene mutagenesis.