Microphytobenthos are significant primary producers in many coastal systems. It is therefore important to quantify their biomass and productivity. Chlorophyll-a is often used as an index for microphytobenthic biomass. However, complications arise as most studies of sediment properties have been on a millimetre scale, whilst chemical and biological gradients in the surface layers of sediment occur over a microscale. The development of a new technique, the Cryolander (Wiltshire et al., 1997; Wiltshire, 2000), now allows microscale analysis of the sediment surface. Areas of high and low diatom biomass were compared using two coring techniques of different vertical resolution; the Cryolander method, with a vertical resolution of 0·2 mm and plastic core tubes (coarse coring), with a vertical resolution of 5 mm. Results indicated that, except at extreme biomass levels, coarse coring does not detect statistically significant differences in chlorophyll-a between obviously diverse sample sites. This may lead to misinterpretation of seasonal and spatial data when coarse coring is used. Furthermore microscale sectioning allows distinctions to be made between chlorophyll-a measured in the photic zone (photosynthetically active biomass (PAB)) and chlorophyll-a measured below the photic zone (photosynthetically inactive biomass (PIB)), allowing accurate determination of biomass specific primary production.