High-density linkage maps are essential tools for genome analysis of various biological traits. Our developed compact multi-gel system, HEGS (high efficiency genome scanning) is a high-throughput and high-cost-performance electrophoresis apparatus. Using this system, a high-density (average interval 2.3 cM) map with 1 065 AFLP and 63 SSR markers was constructed from recombinant inbred lines of a japonica and indica hybrid in just two months of electrophoreses by a single person. More than 50% of the mapped AFLP markers were commonly polymorphic for several combinations between japonica and indica rice and 15% were applicable for genetically closer crosses between upland and lowland types of japonica rice. This system can be used for rapid analyses of all kinds of markers. © 2009 China National Rice Research Institute.