One hundred and twenty-two AFLP markers were mapped using an IR64 x Azucena rice doubled-haploid (DH) population. The distribution of these mapped markers was monitored across a set of 48 diverse landraces of rice. Strong statistical associations were observed between 960 of the 7381 possible pairs of markers across the diverse material. These 960 strongly associated pairs of markers mapped to the same chromosomes in only 111 cases. The remaining 849 pairs were the result of association between markers found on different chromosomes. More than 21% of these genetically unlinked but strongly associated markers are not randomly distributed across the genome but instead occupy blocks of DNA on different rice chromosomes. Amongst associated blocks, there has clearly been maintenance of combinations of marker alleles across very diverse germplasm. Analyses have also revealed that markers are found in association with performance for each of four quantitative traits in both the diverse landrace material and a DH mapping population. It is proposed that the present data provide strong evidence for the co-adaptation of geographically distinct landraces and that this has resulted over time in the maintenance of 'adaptive gene complexes' involving agronomically important quantitative traits.