Typical of large, oligotrophic lakes, Lake Hövsgöl, Mongolia, exhibits complex morphometry which should support a spatially heterogeneous community of benthic macroinvertrates. The lake also exhibits a broad range of land uses. Based on the variation in land use and complex physical habitat of the lake (e.g. substrate variation and presence of affluent streams in bays), we asked two questions. First, does density of total benthic macroinvertebrates vary between different bays in Lake Hövsgöl? Second, does density of individual benthic taxa vary by bay? Samples collected in 1997, the last year for benthic sampling of the lake, were designed to test for variation in macroinvertebrate density between bays and can now be used to establish baseline variation in density for future studies. A total of 56 Ponar grab samples were analyzed from six bays in Lake Hövsgöl. Results of a general linear model analysis of variance showed that total density of macroinvertebrates varied only slightly between bays of the lake, but that most individual taxa showed significant variation between bays. Variation in density for most taxa was linked to substrate composition rather than other geographic or physical variables in the lake. Recent increases in grazing intensity and ecotourism along the shores should be managed to reduce the nutrient load into the lake to avoid impairment of the benthic biota of this unique, ancient ecosystem.