Onion is an economically important crop cultivated worldwide since ancient times. Over the centuries, domestication and outbreeding have had a significant influence on its genetic pool, leading to a high degree of biodiversity. In this study, using kompetitive allele-specific PCR (KASP) genotyping technology, we explored the genetic variation of 73 onion accessions (including wild species, commercial, and local varieties) from different areas of the world. The SNP dataset inspection returned 375 polymorphic loci with a very low percentage of non-calling sites (0.03%). Eight-nine percent of the onions amplified all polymorphic loci and were considered for a population structure analysis. The ΔK method suggested four populations and enabled the identification of genepools, reflecting the geographical origin of the samples. Through statistical studies, our SNP set has proven to be successful, revealing population-specific alleles and potential candidates for use in future breeding programs. Notably, 74 loci were associated with phenotypic traits (bulbing photoperiod, bulb shape, or bulb color), and 3 loci were identified as putative targets of selection associated with onion improvement. Fifty-three pairs of SNPs were co-inherited, and among them, 17 were both trait-associated and in linkage disequilibrium. In conclusion, the data generated in this study allowed the survey of genetic variability in a heterogeneous and scantily examined germplasm, with repercussions on its exploitation in breeding programs.