To explore the stress effect of naphthalene on the cyanobacteria of different cell size, Microcystis aeruginosa and Synechococcus sp. were exposed to different concentration of naphthalene(0, 0. 01, 0. 1, 1, and 10 mg/L)for seven days. Changes of cell concentration, the content of chlorophyll a, and the chlorophyll fluorescence of algae in these groups were determined to investigate effects of naphthalene on the growth and physiological parameters of two species. Results showed that the growth of Synechococcus sp. was significantly inhibited by the naphthalene during the whole experimental. The chlorophyll a content of Synechococcus sp. declined by 3. 9%-40. 4%(compared with the control). The photosynthetic activity and the potential maximum photosynthetic rate of Synechococcus sp. both depressed due to the naphthalene stress, while its tolerance to strong light was improved. This indicates that Synechococcus sp. has a high sensitivity to naphthalene. On the contrary, the growth and the photosynthetic activity of Microcystis aeruginosa were significantly promoted. However, the synthesis of chlorophyll a in the cells of Microcystis aeruginosa was inhibited.