The construction of genetic linkage maps from intraspecific crosses of bread wheat is slow and difficult due to very limited levels of polymorphism, which hinder the assignment of linkage groups to chromosomes and leave large genomic regions without markers. Simple sequence repeats (SSRs) reveal a higher incidence of polymorphism and are more informative than any other DNA marker, and are therefore considered a marker of choice for self-pollinating crops with little intraspecific polymorphism. However, the availability of SSRs in bread wheat is still limited. In this study, selectively amplified microsatellite (SAM) analysis was used to develop informative SSR markers to assist in the construction of an intraspecific wheat map. Three markers were developed for under-represented regions in the genetic map, and 7 for unassigned linkage groups. The latter SSRs permitted the chromosomal origin of 4 unassigned linkage groups to be determined. These results demonstrate the utility of SAM analysis for the targetted development of informative SSR markers to genomic regions of interest, and assignment of linkage groups to chromosomes. Furthermore, SAM analysis facilitates the development of markers for relatively short (<11) dinucleotide repeat sequences, a class of SSRs generally inaccessible to traditional hybridisation-based methods used to develop these markers.