Primula obconica is a perennial herbaceous flower of the Primulaceae that exhibits a distinct heterostyly. Long(L)- and short(S)- styled morphs differ substantially in various ways, and these variations can have a direct impact on how plants regulate their genetic makeup. We can improve the genetic breeding of heterostyly plants by understanding their differences and genetic principles. This trial of P. obconica as a material and morphological observation, cross-fertilization characteristics, and ISSR molecular markers were carried out to analyze the difference in distyly comprehensively. The findings demonstrated that the pollen, stigma, and other floral characteristics of L- and S-morphs varied. The affinity of the both morphs also differed, the L- and S-morphs of inter-pollination had high fruition rates, and pollen and stigma showed compatibility. Under illegitimate pollination, the L-morphs showed partial fitness, while the S-morphs showed complete heteromorphic incompatibility. The ISSR analysis also revealed that 13 primer pairs were polymorphic, clearly banded, and stable, showing significant differences in molecular markers for different morphs. Our study reveals the differences between the morphs of the Primula, which can provide a basis for genetic evolution and breeding work on heterostyly.