Fall-sown barley will be increasingly important in the era of climate change due to higher yield potential and efficient use of water resources. Resistance/tolerance to abiotic stresses will be critical, and foremost among the abiotic stresses is low temperature. Simultaneous gene discovery and breeding will accelerate the development of agronomically relevant fall-sown barley germplasm with resistance to low temperature. We developed two doubled haploid mapping populations using two lines from the University of Nebraska (NE) and one line from Oregon State University (OR): NB3437f/OR71 (facultative × facultative) and NB713/OR71 (winter × facultative). Both were genotyped with a custom 384 oligonucleotide pool assay (OPA). QTL analyses were performed for low temperature tolerance (LTT) and vernalization sensitivity (VS). The role of VRN-H2 in VS was confirmed and a novel alternative winter allele at VRN-H3 was discovered in the Nebraska germplasm. FR-H2 was identified as a probable determinant of LTT and a new QTL, FR-H3, was discovered on chromosome 1H that accounted for up to 48 % of the phenotypic variation in field survival at St. Paul, MN, USA. The discovery of FR-H3 is a significant advancement in barley LTT genetics and will assist in developing the next generation of fall-sown varieties.