Olive (Olea europaea, subsp. europaea, var. europaea) is an iconic tree of the Mediterranean area. One major consequence of climate change is the increasing temperatures. Rising temperatures impact flowering time and synchronization, potentially affecting pollination success. This may negatively impact fruit production in olive trees. Studying the genetic basis of flowering time could provide new insights into the olive tree's adaptation to future climatic conditions. In this study, we aimed to characterize a cultivated olive collection that is assumed to be relevant to conduct genome-wide association studies (GWAS) of flowering time, based on phenotyping data collected over six years. We performed a new genotyping approach on 331 olive cultivars maintained in the Worldwide Olive Germplasm Bank of Marrakech, Morocco (WOGBM). A Capture-based sequencing approach was performed, resulting in 116,676 high-quality SNPs for 318 olive cultivars. Three genetic clusters were structuring the studied collection. The clusters corresponded to the different geographical origins of cultivars, with significantly different flowering time distributions. The data sets now available, including both genetic and phenotypic information, represent a reliable resource for conducting GWAS on flowering time in olive tree.