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The objective of this work was to estimate the changes in abundance and composition of phytoplankton in a coastal lagoon in Baja California, México during neap-spring tide conditions. Sampling was conducted from the 7th to the 16th of October 2004. Surface water was collected at 18 stations distributed across the bay during day time at high tide. Also, a time series was collected at a fixed station; surface water was collected every two hours from 8:00 to 18:00. High temperatures, low salinities and low nutrient concentrations at the oceanic end indicated weak or non upwelling conditions during this period. The phytoplankton community was characterized using an inverted microscope and the chemical taxonomy program CHEMTAX, based on pigment concentration estimated by high performance liquid chromatography (HPLC). The phytoplankton concentration was two times lower during this period than during periods of upwelling in the same year. Cryptophytes and diatoms were the most abundant groups estimated by CHEMTAX. Statistical analyses of the effect of tidal conditions on phytoplankton composition indicate that Zone A is strongly affected by tides, and that tidal effects are lessened at the inner zones. Differences in phytoplankton abundance between zones and between tidal conditions indicate that phytoplankton distribution is patchy in the lagoon.