Pearl millet, a cereal that originated in the Sahel zone of west Africa, can tolerate dry conditions and low soil fertility. It is an important dry land crop, predominantly in Africa and Asia where it is a staple food grain. In the US, pearl millet is primarily used as a forage crop. A new genetic map of pearl millet was constructed based on 180 recombinant inbred lines (RILs) derived from an intraspecific cross between Tift 99B and Tift 454. The map contains 468 molecular markers (361 AFLP and 107 SSR), spans 757 cM, and covers all 7 linkage groups that represent the 7 chromosomes of pearl millet. In addition to using publicly available SSRs, we are also reporting 144 new pearl millet SSRs developed from expressed sequences tags (ESTs) for which probable functions have been recorded. Root-knot nematodes, Meloidogyne spp, are significant pests of cotton and peanut in the southeastern United States. Because pearl millet are potential rotation crops for cotton and peanuts, knowledge of nematode resistance and its inheritance is important for breeding pearl millet with root-knot nematode resistance. In this research, quantitative trait loci (QTL) analysis was conducted to locate the genes for resistance to the southern root-knot nematode [Meloidogyne incognita (Kofoid and White) Chitwood]. One major QTL, QMi-LG2, has a LOD of 14 and explains 32.0% of the phenotypic variance. This QTL for nematode resistance was located in a distal region of pearl millet LG2. An expressed sequence tagged simple sequence repeat (EST-SSR) marker ICMP 3029 (ori) was found to be tightly linked to the QTL and can be useful in marker-assisted selection for nematode resistance in pearl millet breeding.Using this map, we also mapped quantitative trait loci (QTLs) for the agronomic traits of plant height, hundred seed weight, heading date, panicle length, and panicle width to verify the utility of the genetic map.