Pepper ( Capsicum annuum ) is a vegetable with vitamins and minerals which being used as a drug as well as nutritional usage. The plant could be propagated from hybrid seeds. Tissue culture technique could rapidly propagate this plant with a homogeneous genetic structure in a large scale. The application of modern biotechnology for improvement of pepper productivity requires an efficient in vitro plant regeneration protocol. An attempt was made in this study to evaluate the effectiveness of different genotypes (12 genotypes of bell peppers, two sweet peppers and one ornamental pepper), growth regulators and explants (leaves and cotyledons) on callus production and regeneration and introduce appropriate protocol for micropropagation of a commercial variety of pepper in Iran. Analysis of variance indicated that the effectiveness of different genotypes, interaction of various explants and combination of hormones and interaction between genotypes, explants and hormones were significant on the evaluated traits at 1% level. Therefore, in micropropagation protocols different genotypes, explants and compound of hormones should be considered. The results obtained in this research confirmed the synergistic effect of the combination of BAP with IAA in the regeneration of adventitious shoots previously observed by other authors. Among the 15 varieties tested, Lirica, 35-906 RZ, Orange Max, Zamboni, Olite and Ganga were given the best shoot differentiation response (average over 14 shoots per explant) from the leaf- explants. In summary, for micropropagation of pepper with cotyledons and leaves combination of 5 mg/l BAP and 1 mg/l IAA was selected. Elongation of regenerated shoots has been promoted with gibberellic acid (GA 3 ) (1 mg/l) supplemented medium. In this study, at least 80% of the plants regenerated in vitro survived the acclimation period. Somaclonal variation reduced the commercial value of plants. Thus, it is very important to detect somaclonal variation at earlier stage of plant growth to avoid economic loss. The basic objective of micropropagation is to produce the true to- type plants, therefore it is important to certify and retain the fidelity of produced regenerants. Considering high efficiency of leaf explants regeneration, 48 leaf- regenerated plants in 5 genotypes, according to their regeneration yield and appearance, were selected for genetic stability evaluation. Somaclonal variation was studied by 10 pairs of SRAP (Sequence-related amplified polymorphism) primers. The average of amplified scoreable bands of each primer was in range of 10 (E1M1 and E1M3) to 26 (E5M4). The banding patterns of these primer pairs were polymorphic averaged from 0% (E5M3 and E1M1) to 12.9% (E6M5). Among these tested groups, the percentage of polymorphic fragments averaged from 2.8% (Zamboni) to 7.69% (Orange Max). These results clearly indicated that the off type regenerants are produced