Onion and garlic are major Allium vegetables grown worldwide and valued for their culinary, nutritional, and health benefits. However, genetic and molecular improvements in these crops have been challenging due to their complex genetic makeup characterized by high inbreeding depression, biennial life cycles, outcrossing nature, along with large and complex genomes. Understanding recent advancements in Allium molecular genetics is vital for advancing production, quality, and disease resistance. This chapter provides an in-depth review of Allium crop genetics with a particular focus on quantitative trait loci (QTL) mapping of key agronomic traits, highlights the existing challenges, and explores future opportunities for advancing breeding strategies. Utilization of advanced genomic technologies like genetic mapping, RNA sequencing, and third-generation long-read sequencing, along with new population genomics strategies offers exciting opportunities for accelerating genetic gains in Allium crops.