Medicago truncatula (barrel medic) has emerged as a model legume and accession A17 is the reference genotype selected for the sequencing of the genome. In the present study we compare the A17 chromosomal configuration with that of other accessions by examining pollen viability and genetic maps of intraspecific hybrids. Hybrids derived from crosses between M. truncatula accessions, representative of the large genetic variation within the germplasm collection, were evaluated for pollen viability using Alexander's stain. Genetic maps were generated for the following crosses: SA27063 x SA3054 (n = 94), SA27063 x A17 (n = 92), A17 x Borung (n = 99) and A17 x A20 (n = 69). All F(1) individuals derived from crosses involving A17 showed 50% pollen viability or less. Examination of the recombination frequencies between markers of chromosomes 4 and 8 revealed an apparent genetic linkage between the lower arms of these chromosomes in genetic maps derived from A17. Semisterility and unexpected linkage relationship are both good indicators of a reciprocal translocation. The implications of the A17 distinctive chromosomal rearrangement on studies of genetic mapping, genome sequencing and synteny between species are discussed.