Nanotechnology creates opportunities to improve the micropropagation of horticultural plants. The aim of this study was to test the effects of zinc oxide submicron particles (ZnO SMPs), and nanoparticles (NPs) such as ZnO NPs, and ZnO+Ag NPs, at the concentrations of 100, 200, or 400 mg·L<sup>−1</sup>, on the growth parameters of Chrysanthemum × morifolium (Ramat.) Hemsl. ‘UTP Burgundy Gold’ and ‘UTP Pinky Gold’ plantlets propagated by shoot-tip culture on MS medium. Control shoot culture (without SMPs or NPs) and culture with auxin (MS with indole-3-acetic acid IAA) were also evaluated. Treatments with SMPs, NPs, and IAA stimulated the formation of leaves. Most often, plantlets treated with SMPs and NPs, especially with 100 and 200 mg·L<sup>-1</sup> ZnO SMPs, 100 mg·L<sup>-1</sup> ZnO NPs 1.5% H2O, and 100 mg·L<sup>-1</sup> ZnO+1% Ag NPs 1.5% H<sub>2</sub>O, produced leaves with the highest area, perimeter and horizontal width, compared to the control and the IAA treatment. Generally, shoot fresh and dry weights of plantlets treated with SMPs, NPs or IAA were higher compared to the control. The highest shoot fresh and dry weights were stated for 400 mg·L<sup>-1</sup> ZnO+1%Ag NPs 6% H2O and 100 mg·L<sup>-1</sup> ZnO SMPs, respectively, whereas the lowest shoot fresh and dry weights were found for 400 mg·L<sup>-1</sup> ZnO+1%Ag NPs 1.5% H<sub>2</sub>O. The highest values of root system fresh and dry weights were reported for IAA. Contrary, application of 400 mg·L<sup>-1</sup> ZnO+0.1%Ag NPs 6% H<sub>2</sub>O, ZnO+1%Ag NPs 1.5% H<sub>2</sub>O, and ZnO+1%Ag NPs 6% H<sub>2</sub>O resulted in the lowest fresh and dry weights of root systems. The auxin treatment also resulted in the highest length, area, and volume of the root system, as well as root diameter and number of root tips and forks. Nevertheless, the treatments with ZnO SMPs and ZnO NPs most often increased the root system parameters against ZnO+Ag NPs. The results are of scientific and practical importance for modulating chrysanthemum plantlets’ architecture during micropropagation.