Light adaptive strategies were studied in a comparative analysis of the congeneric seagrass species Zostera muelleri and Zostera marina at two case study areas in New Zealand and Germany. Surveys in intertidal seagrass meadows were conducted from pre-dawn until sunset on days when either low or high tide coincided with noon. The results show marked fluctuations of photophysiology (optimum and effective quantum yield, non-photochemical quenching, cycling of xanthophyll cycle (XC) pigments) over daily and tidal cycles. At both locations, we observed a near complete conversion (de-epoxidation) of violaxanthin to zeaxanthin at times with high irradiance and a rapid and complete re-epoxidation under subsequent lower light conditions. At the New Zealand site we also observed significantly larger XC-pigment pool sizes in seagrass leaves sampled in a week when low tide coincided with noon (larger daily fluence and higher maximum irradiance), compared with leaves sampled in a week when high tide was at noon. This dynamic adjustment of xanthophyll pool size has not been previously reported for intertidal seagrasses. It adds to our understanding of an important adaptive feature in a highly dynamic light environment and to the general ecology and adaptability of seagrasses.