The different forms of flowers in a species have drawn thoughtful attention of many evolutionary botanists, including Charles Darwin. Common buckwheat (Fagopyrum esculentum Moench.) is regarded as a dimorphic self-incompatible plant which bears either a pin or a thrum flower. It is revealed that the S supergene the key element to govern the self-incompatibility, flower morphology, and pollen size. Already, we have produced self-incompatible buckwheat lines by an interspecific cross between F. esculentum and F. homotropicum by using embryo rescue. We also notice that the self-compatibility allele, Sh, keeps up the heteromorphic incompatibility. In the past decades, two dimensional gel electrophoresis based proteomics approaches have been applied systematically to identify and profile proteins expressed during pollen development of model plant species. Proteome techniques have vastly been applied in the fields of plant genetics, plant development, and plant physiology and ecology to reveal plant genetic diversity, plant development, differentiation of plant tissue and organ, separation and functional identification of novel component of various organelles, mechanisms of plant adapted to abiotic or biotic stresses including high temperature, low temperature, high salt, drought, and pathogens and insects, and interaction of plant with microbe. However, the plethora of studies related to heteromorphic has added remarkably to our knowledge in the field of the multiple aspects of the breeding system and many researches have provided evidence for the connection between these two components. But in spite of its potential biological significance, the high throughput proteomics analysis of this connection has so far been grossly overlooked. So our attempts are to unravel the proteome investigation in common buckwheat.