Although the majority of horticultural crops are mycorrhiza-dependent, the role of arbuscular mycorrhizal (AM) inoculation in plant production has been neglected in high-input agriculture. Field application of a commercial inoculum mix of Glomus spp. was tested in spice pepper (Capsicum annuum L. var. longum), cv. Szegedi, cultivation. With polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP), differences in small subunit ribosomal RNA genes were used to characterize groups of arbuscular mycorrhizal fungi (AMF) with respect to effects of mycorrhizal inoculation on an indigenous AMF population. The AMF inoculant was able to establish in the rhizosphere of pepper plants and mycorrhizal inoculation increased yield of spice pepper by more than 65% compared with the non-treated control plants. Having relatively high root colonization in the control, non-inoculated treatment indicated high presence of indigenous populations of AMF in the field soil. Although the inoculation affected structure of the resident AM fungal community, it did not influence the composition of AMF associated with pepper roots significantly.