Technical Abstract: The commercial production of onion inbreds, hybrids, and open-pollinated cultivars would benefit from a robust set of molecular markers that confidently distinguish among elite germplasms. Large-scale sequencing of expressed and genomic sequences have revealed that single nucleotide polymorphisms (SNPs), short insertion-deletion (indel) events, and simple sequence repeats (SSRs) are relatively abundant classes of codominant DNA markers. We identified 398 SNPs, indels, and SSRs among 35 elite onion populations and observed that all populations could be distinguished. Phylogenetic analyses of simple-matching and Jaccard's coefficients for SSRs produced essentially identical trees and relationships were consistent with known pedigrees and previous marker evaluations. The SSRs revealed that elite germplasms from specific companies or breeding programs were often closely related. However phylogenetic analyses of SNPs and indels did not reveal clear relationships among elite onion populations and there was no agreement among trees generated using SNPs and SSRs. This discrepancy could be due to SNPs and indels in duplicated regions of the onion genome (paralogs). Nevertheless, these PCR-based markers will be useful in the quality control of inbred and hybrid seed lots.