We report the establishment of a large maize SNP array and its use for diversity analysis and high density linkage mapping. The selected markers were preferentially located in genes and evenly distributed across the genome. The array was tested with a set of maize germplasm including various inbred lines, parent/F1 combinations, and distantly related teosinte material. A total of 49,585 markers, including 33,417 within 17,520 different genes, were of good quality for genotyping, with an average failure rate of 4%. To demonstrate this array's use in genetic mapping and for the independent validation of the B73 sequence assembly, two intermated maize recombinant inbred line populations -- IBM (B73xMo17) and LHRF (F2xF252) -- were genotyped to establish two high density linkage maps with 20,913 and 14,524 markers respectively. 172 mapped markers were absent in the current B73 assembly and their placement can be used for future improvements of the B73 reference sequence. Colinearity of the genetic and physical maps was mostly conserved with some exceptions that suggest errors in the B73 assembly. Five regions containing non-colinearities were identified on chromosomes 2, 3, 6, 7 and 9, and are supported by both independent genetic maps. Four additional non-colinear regions were found on the LHRF map only; they may be due to a lower density of IBM markers in those regions or to true structural rearrangements between lines. Given the high quality of the array, it will be a valuable resource for maize geneticists and breeders.