Transposable elements (TEs), are a rich source for molecular marker development as they constitute a significant fraction of the eukaryotic genome and impact the overall genome structure. Here, we utilize Mutator-based transposon display (Mu-TD), and CACTA-derived sequence-characterized amplified regions (SCAR) anchored by simple sequence repeats and single nucleotide polymorphisms to locate quantitative trait loci (QTLs) linked to agriculturally important traits on a genetic map. Specifically, we studied recombinant inbred line populations derived from a cross between dent corn and waxy corn. The resulting linkage map included 259 Mu-anchored fragments, 34 SCARs, and 614 SSR markers distributed throughout the ten maize chromosomes. Linkage analysis revealed three SNP loci associated with kernel starch synthesis genes (sh2, su1, wx1) linked to either Mu-TD loci or SSR markers, which may be useful for maize breeding programs. In addition, we used QTL analysis to determine the chromosomal location of traits related to grain yield and kernel quality. We identified 24 QTLs associated with nine traits located on nine out of ten maize chromosomes. Among these, 13 QTLs involved Mu loci and two involved SCARs. This study demonstrates the potential use of DNA transposon-based markers to construct linkage maps and identify QTLs linked to agronomic traits.