Advances in next generation sequencing technologies have enabled researchers to do in depth genome studies. The steadily decreasing cost of sequencing has made it possible to conduct a Genotyping-by-Sequencing (GBS) approach both in plants and animals. A reliable and efficient genotyping protocol is crucial for studying and understanding the genetics and genomics of sorghum. The current work aimed at investigating the applicability of Genotyping-by-Sequencing techniques in a sorghum mapping population generated between sweet stem and grain sorghum parents. Two methods of Genotyping-by-Sequencing, whole genome shotgun (WGS) and restriction-site associated DNA (RAD) methods were used to examine the sorghum genome in this study. A total of 921 031 and 3 119 variants (SNPs and INDELs) were identified in WGS and RAD sequencing approaches respectively using CLC Genomics Workbench 6.0.1. The Trait Analysis by aSSociation, Evolution and Linkage (TASSEL) pipeline identified a total of 2 701 814 and 17 012 in the WGS and the RAD sequencing approach respectively. The TASSEL pipeline identified 1 456 253 and 3 435 variants from the two parents in the WGS and the RAD sequencing approach respectively. The results revealed the RAD method as the better Genotyping-by-Sequencing approach for large populations and Trait Analysis by aSSociation, Evolution and Linkage as the best data analysis tool as it discovered more variations than CLC Genomics Workbench. The development of a precise and inexpensive Genotyping-by-Sequencing protocol serves as a robust framework to which sorghum populations can be characterized. These results will contribute towards genetic mapping of the markers and subsequent identification of quantitative trait loci (QTLs) governing different traits of interest contributing towards breeding for feedstock varieties that are optimized for biofuel production from sorghum.