Age-related macular degeneration, which is the leading cause of blindness in industrialized countries, is a multifactorial, degenerative disorder of the macula with strong heritability. For age-related macular degeneration in humans, the genes ARMS2 and HTRA1 in the region 10q26 are both promising candidates for being involved in pathogenesis. However, the associated variants are located in a region of strong linkage disequilibrium and so far, the identification of the causative gene in humans was not yet possible. This dilemma might be solved using an appropriate model organism. Rhesus monkeys suffer from drusen, a major hallmark of age-related macular degeneration, and the drusen-phenotype shares susceptibility factors with human macular degeneration. Thus, the rhesus monkey represents a natural animal model to uncover genetic factors leading to macular degeneration. Moreover, the existence of genetically homogenous cohorts offers an excellent opportunity to determine risk factors. However, the 10q26-orthologue genomic region in rhesus monkeys is not characterized in detail so far. Therefore, the aim of this study is to analyze the rhesus linkage disequilibrium structure and to investigate whether variants in ARMS2 or HTRA1 are associated with the drusen-phenotype as well. We sequenced parts of a 20 kb region around ARMS2 and HTRA1 in a genetically homogeneous cohort of 91 rhesus monkeys descending from the CPRC rhesus cohort on Cayo Santiago and currently housed in the German Primate Centre in Göttingen. Within this group, ophthalmoscopic examinations revealed a naturally high drusen prevalence of about 47% in monkeys >5 years. We detected 56 genetic variants within and around ARMS2 and HTRA1 and, as one deviates from Hardy-Weinberg-Equilibrium, 55 polymorphisms were used to generate a linkage disequilibrium-Plot and to perform association studies. We observed strong linkage disequilibrium between the markers and were able to define two haplotype blocks. One of these blocks spanned the whole ARMS2 locus and the 5' part of HTRA1 - almost perfectly resembling the situation found in humans. Tests for association revealed a variant in the promoter region of HTRA1 and two variants in the 5'-UTR of ARMS2 to be associated with drusen. The strong linkage disequilibrium inhibits - as in humans - a determination of the risk gene using statistical methods only. However, the conserved linkage disequilibrium structure in humans and macaques goes in line with the recently emerged dual causality model proposing that ARMS2 and HTRA1 are functionally connected and that both genes contribute to the disease pathology. Moreover, the characterization of the 10q26-orthologue genomic region of the rhesus monkey provides a basis for now needed functional investigations in a well-characterized model organism.