The genetic wealth of range-restricted species is threatened by human activities such as habitat fragmentation or alteration. This research focused on the genotype effect in sexual propagation with freshly collected seeds of vulnerable local endemic plants in Crete, namely, Campanula pelviformis and Petromarula pinnata (Campanulaceae), which can be sustainably utilized for agro-alimentary, medicinal, and ornamental purposes. The morphological characteristics of seed length, width, and weight of freshly collected seeds from five wild-growing populations of C. pelviformis and seven wild-growing populations of P. pinnata from lowlands (<500 m) and semi-mountainous (>500 m) altitudes were measured and subjected to germination experiments at four incubation temperature treatments (10, 15, 20, and 25 °C). The effects of temperature, genotype, and their interactions were statistically significant for seed germination, with the results similar to those of previous studies on stored seeds of the same populations. Freshly collected seeds of both species germinated best at incubation temperatures of 10 °C and 15 °C (>68.13% for all population of C. pelviformis and >80.63% for six out of seven populations of P. pinnata), while significant differences were detected among genotypes for both species at each incubation temperature and among genotypes, even from similar altitudes. A statistically significant effect of altitude on germination percentages was observed at an incubation temperature of 20 °C between lowland and semi-mountainous genotypes for both species. The data produced in this study may enhance conservation efforts and lead to species-specific information that can be exploited in the future for their introduction as novel multi-purpose crops.