In order to excavate the beneficial microorganism resources in salted pepper and further improve the quality control of salted vegetables. The community composition and relative abundance in the salted pepper were explored by 454 pyrosequencing technology. The results showed that fungi with known classification status in salted C. annuum L. var. dactylus M could be assigned to 2 phyla， 13 classes， 17 orders， 31 families， 45 genera and 87 species. Fungi with known classification status in salted C. annuum L. var. conoides Irish could be assigned to 1 phyla， 1 class， 2 orders， 2 families， 2 genera， and 1 species. The dominant phyla in salted C. annuum L. var. dactylus M were Ascomycota （73.63%） and Basidiomycota （23.42%）. Ascomycota （99.96%） was the only phylum with known classification status in salted C. annuum L. var. conoides Irish. The dominant genera in salted C. annuum L. var. dactylus M were Pichia （25.78%）， Alternaria （21.85%）， Hannaella （10.5%）， Candida （7.82%）， Cryptococcus （6.92%） and Cladosporium （6.27%）. The dominant genera in salted C. annuum L. var. conoides Irish was Candida （93.49%）. The microbial diversity of salted line pepper and salted rice pepper was significantly different， and the microbial diversity index of salted line pepper was higher than that of salted rice pepper.