Variability of chlorophyll (as an index of micro-algal abundance) between warm and cool seasons at different heights on (distances across) the shore was investigated on intertidal mudflats in warm-temperate Australia. Chlorophyll was measured using ratios of reflectances from field spectrometry and minimal fluorescence (F0) from PAM fluorometry to compare patterns obtained using these two methods. A single sampling period comprised 2 days of sampling, one for each mudflat, with 2 sampling periods nested within each month, 2 months within each of a cool and warm season in each of 2 years. Large differences in amounts of chlorophyll were found between the two mudflats, although spatial and temporal patterns of variation were generally similar. There were greater amounts of chlorophyll in the cooler months than in the warmer months in each location in each year, which contrasts with many of the patterns reported from elsewhere. There was more chlorophyll on the upper than on the lower shore and the increases from summer to winter were generally greater at the higher levels. Large variation in chlorophyll from week to week within each month demonstrated the need for adequate replication in studies of seasonal patterns of variability. Measurements made by a field spectrometer and a PAM fluorometer were largely consistent, but, at certain times, they showed an opposite pattern. The reasons for these differences were investigated further by looking at differences in other pigments, but the different results from the two methods could not to be explained by changes in composition of the micro-algal assemblage and, as yet, remain unexplained.