It is estimated that world-wide existing germplasm collections contain about 7.4 million accessions of plant genetic resources. Wheat (Triticum and Aegilops) represents the biggest group with about 900,000 accessions. One of the largest ex situ genebanks worldwide is located at the Leibniz Institute of Plant Genetics and Crop Plant Research in Gatersleben, Germany. This collection comprises wild and primitive forms, landraces as well as old and more recent cultivars of mainly cereals but also other crops. As on the global scale wheat is the largest group having almost 30,000 accessions. Beside the long term storage and frequent regeneration of the material phenotypic characterisation and evaluation data are collected as a prerequisite for gene identification and mapping. We report the outcome of an association-based mapping study to elucidate the genetic basis of flowering time in winter wheat. A core collection of 96 cultivars was subjected to a genome-wide scan using diversity array technology markers. The same set of accessions had been earlier evaluated for flowering time over six consecutive seasons. Some of the resulting marker-trait associations (MTAs) mapped to chromosomal locations in which known major genes affecting flowering time are known to reside. However, most of the MTAs identified genomic locations where no such genes are known to map, so providing new opportunities to exploit genetic variation for flowering time in wheat breeding programmes.