Winter wheat (Triticum aestivum L.) production in high latitude growing regions is often limited by harsh winters that can lead to significant reduction in crop stands and thus yield. Winter survival is a complex trait because winterkill is the result of several interacting abiotic and biotic stress factors that lower the survival during winter including freezing temperature, freezing-induced dehydration, frost heaving, ice encasement and snow mold. To identify key genetic factors that contribute to higher winter survival under field conditions, we characterized the winter survival of a diversity panel of 450 Canadian wheat varieties in Eastern Canada. Next-generation image-based phenotyping methods including unmanned aerial vehicle (UAV) and ground-level imagery were used to characterize the panel and to more accurately quantify winter survival differences among genotypes. Genome-wide association studies resulted in the identification of nine quantitative trait loci (QTLs) for winter-survival including Frost Resistance-1 (Fr-1) and Fr-2. By using the recently released annotated sequence of the wheat genome and the publicly available RNA-Seq data, three putative candidate genes for winter-survival were identified on chromosomes 4A, 4B and 5A. In addition, the panel was genotyped for allele variation of candidate genes that have been mapped close to the identified QTLs. This includes Vernalization-A1 (Vrn-A1), C-Repeat Binding Factor (CBF)-A12 and -A15 on chromosome 5A. Collectively, our study provides an example in applying next-generation tools in phenotyping integrated with application of novel genomics tools to successfully identify putative candidate genes that are associated with winter survival in wheat. We also demonstrate that having the frost tolerant haplotype at CBF-A12 and -A15 and higher number of copies of VRN-A1 (3) will contribute to higher winter survival of winter wheat in Eastern Canada. The complexity of winter stress in the field makes our study a valuable complement to frost tolerance studies in the identification of genetic factors that can contribute to stable winter wheat production in high latitude growing region.