The daffodil Narcissus pseudonarcissus L. contains alkaloids of pharmaceutical interest. Wild daffodil populations have diverse genetic backgrounds and various genetic traits of possible importance. Developing protocols for plant production from seeds may ensure the availability of a large reservoir of individuals as well as being important for species with bulbs that are difficult to acquire. The closely related Narcissus pseudonarcissus subsp. munozii-garmendiae and subsp. nevadensis were investigated in this study because the alkaloids isolated from both are of high pharmacological interest. At the dispersal time, the seeds of both were dormant with underdeveloped embryos, i.e., morphophysiological dormancy (MPD). Experiments were conducted outdoors and under controlled laboratory conditions. Embryo growth and the percentages of radicle and seedling emergence were calculated under different temperature–light stratifications. In N. munozii-garmendiae, embryo growth occurred during warm stratification (28/14 °C or 25/10 °C) and the radicle then emerged when the temperature decreased, but the shoot was dormant. In N. nevadensis, the seeds germinated when cold stratified (5 °C) and then incubated at cool temperatures. Thus, N. munozii-garmendiae and N. nevadensis exhibit different levels of MPD, i.e., deep simple epicotyl and intermediate complex, respectively. Plant production protocols from seeds were established for both taxa in this study.