Shoot-to-landscape scale sources of variation in photosynthetic characteristics of Thalassia testudinum, as measured in situ using a submersible pulse-amplitude modulated fluorometer (diving-PAM), were investigated. Shoot-scale variation was assessed to develop a standard-methods protocol for this species. Significant within-shoot and among-shoot scale variation was observed for several PAM-fluorescence parameters. The fraction of incident photosynthetically active radiation (PAR) absorbed by rank 1 (youngest) leaves, 0.67 +/- 0.03, was significantly lower than the PAR absorbed by rank 2 and 3 leaves (0.78 +/- 0.04 and 0.77 +/- 0.04, respectively). Quantum yields (Y) and photosynthetic efficiency (F-v/F-m) exhibited greater variability and generally decreased with increasing leaf age (Y = 0.78 +/- 0.02, 0.78 +/- 0.03, and 0.76 +/- 0.06 and F-v/F-m = 0.79 +/- 0.02, 0.77 +/- 0.5, and 0.75 +/- 0.06 for rank 1, 2, and 3 leaves, respectively). Maximum fluorescence of light-acclimated leaves (F'(m)) significantly decreased from the base to the tip of leaves (1032 203, 1059 139, and 793 107 for the base, middle and tip of the leaf) and Y was significantly reduced from 0.68-0.76 to 0.27-0.62 when measured where leaf lesions were present. However, paired comparisons (with versus without lesions at the tip of the leaf) for the base, middle, and tip areas of rank 2 leaves indicated that lesions effects on photosynthesis were localized only to the area of the lesion (tip). The Y exhibited relatively high variability for short-shoots within seagrass die-off patches and were significantly reduced for short-shoots exhibiting die-off symptoms (rotten leaf base grayish-green leaf color, but no lesions). Negative response slopes for Y and F-v/F-m measured as part of a landscape-scale sampling program, revealed the presence of significant diurnal (time-of-day) and photosynthetic photon flux density (PPFD) related variation, with a more negative slope for Y. These results indicate that the selection of leaf tissue, short-shoot location, and time of measurement need to be considered when determining photosynthetic rates for seagrasses in situ. (C) 2002 Elsevier Science B.V. All rights reserved.