The prevalence of lactic acid bacteria (LAB) and the effects of their antimicrobial peptides on H-2 production in anaerobic fluidized bed reactors (AFBRs) operated with cheese whey (AFBR1 and AFBR2) were verified in this study. The AFBR1 received 5 g COD L-1 of cheese whey with decreasing hydraulic retention times (HRT) of 14 to 8 h. The AFBR2 was operated with 3-10 g COD L-1 of cheese whey with an HRT of 6 h. Next, 152 colonies were selected from de Man, Rogosa and Sharpe MRS agar plates, and 45 strains were classified as LAB. The counts oscillated between 6.6 and 8.1 log CFU mL(-1), indicating that the LAB survived and persisted in the AFBRs. Pure cultures were identified using 16S rRNA gene sequencing, and Lactococcus lactis was the prevalent LAB (70%) in both reactors. The highest H-2 yields (1.9 and 2.3 mol H-2 mol lactose(-1)) were obtained during the first operational phase in both reactors when a low organic loading rate (OLR) was applied, and when the growth of Lactococcus spp. was associated with Leuconostoc pseudomesenteroides. The bacteriocin-producing LAB (mostly Lactobacillus spp.) found on the specific phases of reactors AFBR1 and AFBR2 exerted a remarkable influence on H-2 yield. Copyright (C) 2015, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.