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Microspore embryogenesis is widely used in plant breeding to obtain homozygous lines. It is an important way of obtaining haploids and it is valuable for QTL (Quantitative Trailt Locus) mapping and genetic research. We analyzed the microspore embryogenesis ability of 142 recombinant inbred lines (RIL) and mapped QTLs for microspore embryogenesis based on a genetic map constructed using specific-locus amplified fragment sequencing SLAF-seq technology. Results revealed that microspore embryogenesis ability in pepper is a quantitative character. Seven QTLs were detected on linkage groups LG2, LG6, LG8, LG11 and LG12. The peak logarithm of odds (LOD) score of the seven QTLs ranged from 3.51 to 6.66, and the range of phenotypic variation explained by a single QTL ranged from 4.76 to 18.30%. We identified a major QTL, Me2.2, located in the region of 116.5–118.5 cM on LG2; the corresponding physical segment was 166,621,667–167,038,758 bp, and 24 candidate genes were predicted in this region. Functional annotation indicated that these genes are closely related to the initiation of cell division, symmetrical or asymmetric cell division, and other life processes. The study laid a good foundation for further research on the mechanism of microspore embryogenesis. [ABSTRACT FROM AUTHOR]