Colletotrichum sublineola is an aggressive fungal pathogen that causes the disease anthracnose in the bioenergy crop sorghum. The resulting leaf blight and stem rot can cause yield reductions of up to 70%. The sorghum acreage in the southeastern U.S. is increasing steadily due to the species’ ability to produce high yields under limited inputs. Successful cultivation of sorghum in this region, where Colletotrichum sublineola is endemic, is contingent upon anthracnose resistance. We generated a biparental mapping population of 135 F4 and F5 sorghum lines to identify anthracnose resistance genes in the highly resistant line ‘Bk7’. The population was phenotyped in three Florida environments and genotyped by sequencing (GBS) following a customized filtering procedure that retained informative markers. Two resistance loci were identified - on chromosomes 7 and 9 - using association analysis between the GBS-derived markers and phenotype using Fisher’s exact test. Both loci contained multiple candidate resistance genes. Fine mapping of the locus on chromosome 9 was performed on a BC1S1 population generated from four sweet sorghum cultivars derived from the sorghum lines ‘Bk7’ (also used as parent in the abovementioned mapping population) and ‘Mer 81-4’. The efficacy of fine-mapping with PCR-based SNP markers was compared to that using GBS. In both instances the size of the resistance locus could be reduced substantially, but the GBS procedure provided much greater resolution, at a substantially higher cost. This case formed the basis for a comparison of the merits of both genotyping methods under a number of different scenarios (population size, marker density, labor cost) to assist in deciding on the most effective genotyping procedure. Supported by the Southeastern Sun Grant Center/USDA-NIFA Award No. 2010-38502-21854, USDA-BRDI Award No. 2011-10006-30358, and US DOE award No. DE-SC0014439.