I-type lysozymes have been found to play significant roles in the innate immune responses of mollusk. In the present study, the full-length cDNA of an I-type lysozyme (designated RpiLYZ-2) was cloned from Ruditapes philippinarum by RACE approaches. The open reading frame of RpiLYZ-2 was 471 bp and encoded a polypeptide of 156 amino acids. The RpiLYZ-2 transcript was expressed in all detected tissues with the highest expression level in mantle and the lowest expression level in muscle. After being exposed to temperature[(29±1), (21±1), (13±1)℃, salinity (32, 22 and 12) stress and Vibrio anguillarum challenge, the expression of RpiLYZ-1 and RpiLYZ-2 displayed distinct pattern in the detected tissues. After being stimulated by elevated temperature (21℃) or salinity 22 stress, the expression pattern of RpiLYZ-1 transcript was decreased after the initial increase, while the expression pattern of RpiLYZ-2 transcript displayed an opposite trend. After being stimulated by elevated temperature 29℃ or salinity 12 stress, the expression pattern of RpiLYZ-1 transcript was down-regulated as time progressed on, while the expression of RpiLYZ-2 mRNA showed an opposite trend. After being challenged with V. anguillarum, a significant up-regulation of RpiLYZ-1 was observed except 12 h, while the expression of RpiLYZ-2 mRNA was significantly inhibited at the early stage of bacterial challenge and recovered at 72 h. The above results suggested that environmental factors and pathogenic stimulation affected the clam's innate immune responses and the expression of RpiLYZ-1 and RpiLYZ-2, and functional division perhaps existed between RpiLYZ-1 and RpiLYZ-2.