Crop genome sequencing projects generate massive amounts of genomic sequence information, and the utilization of this information in applied crop improvement programs has been augmented by the availability of sophisticated bioinformatics tools. Here, we present the possible direct utilization of sequence data from a sorghum genome sequencing project in applied crop breeding programs. Based on sequence homology, we aligned all publicly available simple sequence repeat markers on a sequence-based physical map for sorghum. Linking this physical map with already existing linkage map(s) provides better options for applied molecular breeding programs. When a new set of markers is made available, the new markers can be first aligned on a sequence-based physical map, and those located near the quantitative trait locus (QTL) can be identified from this map, thereby reducing the number of markers to be tested in order to identify polymorphic flanking markers for the QTL for any given donor × recurrent parent combination. Polymorphic markers that are expected (on the basis of their position on the sequence-based physical map) to be closely linked to the target can be used for foreground selection in marker-assisted breeding. This map facilitates the identification of a set of markers representing the entire genome, which would provide better resolution in diversity analyses and further linkage disequilibrium mapping. Filling the gaps in existing linkage maps and fine mapping can be achieved more efficiently by targeting the specific genomic regions of interest. It also opens up new exciting opportunities for comparative mapping and for the development of new genomic resources in related crops, both of which are lagging behind in the current genomic revolution. This paper also presents a number of examples of potential applications of sequence-based physical map for sorghum.