Cortinarius brunneocarpus var. microsporus is described and illustrated from coniferous forests of District Swat, Pakistan based on morphological characters and phylogenetic analyses of the nuclear rDNA internal transcribed spacer (ITS) region. It is morphologically well-supported by significantly smaller basidiospores which are moderately to densely verrucose and with a suprahilar depression  The new variety has Eurasian distribution and is being reported from Pakistan, Norway and Estonia. Differences between the new variety and similar taxa are briefly discussed.