Global climate change is predicted to increase water precipitation fluctuations and lead to localized prolonged floods in agricultural fields and natural plant communities. Thus, understanding the genetic basis of submergence tolerance is crucial in order to improve plant survival under these conditions. In this study, we performed a quantitative trait locus (QTL) analysis in Arabidopsis to identify novel candidate genes for increased submergence tolerance by using Kas-1 and Col (gl1) parental accessions and their derived recombinant inbred lines (RILs). We measured survival after submergence in dark for a 13-day period and used median lethal time, LT50 values for the QTL analysis. A major QTL, the Come Quick, Drowning (CQD1) locus, was detected in two independent experiments on the lower arm of chromosome 5 involved in higher submergence tolerance in the parental accession Kas-1. For fine-mapping, we then constructed near isogenic lines by backcrossing the CQD1 QTL region. We also analyzed QTL regions related to size, leaf number, flowering or survival in darkness and none of the QTL related to these traits overlapped with CQD1. The submergence tolerance QTL, CQD1, region detected in this study includes genes that have potential to be novel candidates effecting submergence tolerance such as TREHALOSE-6-PHOSPHATE PHOSPHATASE and RESPIRATORY BURST OXIDASE PROTEIN D. Gene expression and functional analysis for these genes under submergence would reveal the significance of these novel candidates and provide new perspectives for understanding genetic basis of submergence tolerance.