The acid adaption is commonly used as a strategy to enhance the acid tolerance of bifidobacteria. However, the acid tolerance response (ATR) mechanism elicited by this method is unclear. Real-time relative-quantitative PCR was applied to analyze the changes in the expressions of ffh, uvrA, groES, and dnaK involved in the ATR after acid-adaptation in Bifidobacterium longum BBMN68 in different growth phases. BBMN68 was cultured at a constant neutral pH during the whole growth phase. Without acid-adaptation, the survival ratios at the lethal pH 3.0 were 0.25% and 17% in the exponential and stationary phases, respectively. The genes ffh, uvrA, groES, and dnaK were significantly higher in the stationary phase than in the exponential phase. The results indicated that although there was no acid stress, the acid tolerance of cells was elevated from the exponential phase into stationary phase. After acid-adaptation at pH 5.0 for 120 min, the survival ratios of BBMN68 in the exponential and stationary phases were increased to 2.5 and 31%, respectively. In the exponential phase, ffh, uvrA groES, and dnaK were significantly decreased after acid-adaptation. In the stationary phase, after acid-adaptation for 15, 60, and 120 min, the genes uvrA, groES, and dnaK were significantly decreased, whereas, ffh was significantly up-regulated at 15 min, and then suppressed at 60 and 120 min after acid-adaptation. The results represented that the ATR in B. longum was different from other bacteria, and ffh may be the transient acid gene.