Several wild sunflower (Helianthus) species important sources of genetic diversity for enhancing the performance of cultivars and single-cross hybrids of common sunflower (H. annuus = ANN; 2n = 2x = 34). Silver-leaf sunflower (H. argophyllus = ARG; 2n = 2x = 34), which diverged 375,000 to 500,000 years before present from ANN, is a source of disease resistance alleles. We developed an ARG mapping population by crossing an outbred individual (ARG1805-1) to a nuclear male-sterile inbred line of ANN (NMS801), screened 1,417 previously mapped DNA markers, and mapped 299 polymorphic loci in the testcross hybrid mapping population (n = 94). Eighteen ARG linkage groups were aligned with ANN and chromosomal rearrangements were identified using 194 orthologous loci. We identified 11 colinear linkage groups, 2 syntenic chromosomes carrying segmental duplications and inversions, and 5 chromosomes carrying non-reciprocal translocations. The reduction in fertility and meiotic abnormalities observed in ANN x ARG hybrids are caused by 6 chromosomal rearrangements which could impede gene-flow.