These data are based on analysis of replicated 1.98 cm2 cores of the pigmented surface layer of benthic microbial mats from Lake Hoare. Parallel experiments in which thicker cores were sectioned showed that this surface layer contained all chlorophyll-a present in the cores. They are expressed per unit area of core, units andmicro;g/cm2 (micrograms per square centimeter). All depths refer to depth from the surface and are in meters. Samples were obtained from an approximately linear transect stretching from the Lake Hoare laboratory complex towards the lake deepspot. Cores were collected through December 1996 by scuba divers. Initially, cores of 7 cm diameter were collected using sharpened perspex coring tubes. After retrieval to the surface, these were subsampled using sharpened, cut-off syringe barrels. Cores were stored at -20anddeg;C, in the dark, until processed in New Zealand some 2-3 months later. Extraction was into 10 ml of 90% acetone (allowing for volume of water in core), and was aided by grinding with a teflon pestle in a glass tube. Calculations were based on absorptance of the extract measured at 665, corrected by subtracting that at 750 nm. Correction for phaeopigments was accomplished by re-measuring absorptance after acidification with dilute HCl. Equations used for calculating chlorophyll-a in andmicro;m/cm2 with (Eq 1) and without (Eq 2) correction for phaeopigments were: Eq 1: (A665(na)-A665(ac)) x 27.3 x 1/vol x 1/area Eq 2: A665(na) x 11.23 x 1/vol x 1/area where A665(na) and A665(ac) are corrected absorptances (as optical density) before and after acidification, vol is volume of acetone used (ml) and area is the area of the core (cm2).