Objective To clarify the separation law of dwarfing traits of pepper and screen the closely linked molecular markers， so as to lay a foundation for MAS breeding of pepper’s dwarfing traits.Methods Seven agronomic and quality traits of pepper dwarf germplasm SSI9024a and infinite growth germplasm Hangjiao were compared， and then four generations of isolated populations were constructed. The traits were preliminarily located by BSA mixed pool sequencing， and SSR molecular markers closely linked to them were screened.Results Among the four agronomic traits such as plant height， fruit length， fruit width and single fruit weight， Hangjiao was significantly better than those of SSI9024a， and the VC content of the latter was more than 6 times that of the former. Genetic analysis showed that the dwarf trait was controlled by a single invisible gene. BSA sequencing located the gene on chromosome 6. Through the verification of individual plants of backcross offspring， primer HpmsE002 was closely linked to the dwarf trait.Conclusions The genetic law of pepper dwarf trait was successfully analyzed， and the closely linked molecular markers were obtained， which can enhance the reference basis for its subsequent MAS breeding.