In April of 2006, the firstgeneration selected group (SG) was established by selecting eleven breeders with yellow shell color in Liusha Bay stock of pearl oyster Pinctada martensii. A control group (CG) was also obtained by randomly selecting fifty mature individuals in the same stock as breeders. In October of 2007, the individuals with the uniform size were separately sampled from the SG and CG groups and differences in physiological indices such as oxygen consumption rate and NH3 excretion rate between the two groups were evaluated at different temperature and salinity levels. The results obtained from this experiment included (1) oxygen consumption rate (OCR) and NH3 excretion rate (NR) were positively correlative to the temperature. Under the test temperatures, the increasing OCR and NR values of the SG covered the range of 0.117-1.009 mg / (g·h) and 0.013-0.028 mg / (g·h), while those of the CG were 0.142-0.827 mg / (g·h) and 0.016-0.028 mg / (g·h). (2) No significant differences of OCR and NR were found in the two groups at 15 ℃ (P> 0.05). At 20, 25 and 30 ℃, however, the SG displayed higher oxygen consumption rate and NH3 excretion rate than the CG, with significant differences observed in oxygen consumption rate at 30 ℃ (P < 0.05). (3)Q₁₀ respiration and )Q₁₀ excretion of the SG were 4.87 and 1.91 respectively; while those of the CG were 3.54 and 1.46. The average O/N ratios of the SG and CG were observed at 20.50 and 19.56. (4)At test salinity of 20-36, OCR and NR of the two groups increased with the increasing salinity, and reached the peak value at salinity of 28, and then the values decreased beyond 28. The OCR of the SG was in range of 0.435 to 0.678 mg / (g·h) while that of the CG was 0.233 to 0.671 mg / (g·h). The NR value of the SG covered the range of 0.011 to 0.027 mg / (g·h), and that of the CG 0.014-0.025 mg / (g·h). (5) At salinity 24, 28, 32 and 36, the SG had higher oxygen consumption rate than the CG, with significant differences observed at salinity 20, 24 and 36 (P < 0.05). The SG had higher NH₃ excretion rate than the CG at salinity 28 and 32, while the SG had lower NH₃ excretion rate than the CG at salinity 20, 24 and 36. (6) At salinity 20-36, the average O/N ratios of the SG and the CG were 34.50 and 25.01 respectively. The present results indicate that there exist evident differences in physiological indices between the SG and CG after one generation selection for yellow color, which will provide some useful information for further breeding in the groups.