The photosynthetic activity of Zostera marina, Zostera asiatica and Phyllospadix iwatensis shoots from populations of Hokkaido (Northern Japan) was determined using the pulse amplitude modulated (PAM) fluorometer. Several fluorescence parameters were measured as a function of irradiance and leaf age: electron transport rate (ETR), quantum yield, photochemical quenching (qP) and non-photochemical quenching (NPQ). The leaf age determined by the leaf position in the shoot bundle strongly influenced the photosynthetic activity of Z. marina, Z. asiatica and P. iwatensis. Young leaves had the maximum electron transport rate (Zm: Leaf 1 = 15.7, Leaf 2 = 16.3; Za: Leaf 1 = 13.0, Leaf 2 = 12.2; and Pi: Leaf 1 = 12.5, Leaf 2 = 11.7) and showed higher photoprotection (NPQ) than old leaves. Among the studied seagrass species, Z. marina had the highest photosynthetic activity (ETRmax = 15.3), in accordance with the highest production in the field in comparison with the other two seagrass species. The PAM fluorometry technique showed to be effective in determining intraspecific (among-leaves) and interspecific (among-species) variation in seagrass photosynthetic activity.