H. pylori infection of rhesus macaques is under independent selective pressure for loss of babA and overexpression of babB. Five or six rhesus macaques were inoculated with the H. pylori J166 babA::cat (A, B) or babB::cat (C, D) mutant, and multiple output colonies from 2, 8, 14, and 20 weeks p.i. were examined. Amplification and sequencing were used to determine if the gene at the babA locus was babA::cat (A) or babB (B) for monkeys inoculated with the babA::cat mutant or if it was babA (C) or babB::cat (D) for monkeys that received the babB::cat mutant. Sequence analysis was also used to determine if the CT repeat region was in frame (eight CT repeats, black bars) or out of frame (seven or nine CT repeats, hatched bars). Loss of BabA expression by gene conversion in the babA::cat mutant (B) and by phase variation in the babB::cat mutant (C) suggests that there is independent selective pressure against expression of BabA and for overexpression of BabB.