High throughput genotyping technologies, such as SNP genotyping arrays that have emerged in recent years, have revolutionized the way we can analyze the origin and genetic control of traits in crops and have proven to be high-throughput and cost-effective tools. I developed Affymetrix™ Axiom® Citrus HD Genotyping Array and Affymetrix™ Axiom® Citrus Genotyping Array with 1.4 M and 58 K autosomal SNPs. DNA from 924 citrus accessions was hybridized to one or both of these arrays and yielded an extensive genomic inventory of the Citrus Variety Collection (CVC). High concordance was generally observed between DNA sequence and array data, and a simulation study suggested that errors in the range observed in more distant taxa have little to no effect on analyses such as principal component analysis (PCA), phylogeny and admixture analysis. This data was also exploited in a systematic study of genetic diversity, including phylogeny, admixture, and patterns of introgression at the chromosomal level. The study identified non-admixed accessions belonging to citrus progenitor species, and revealed the scale of diversity found in the CVC. Putative ancestors were identified for the identified admixed accessions and many species named by Tanaka were found to be hybrids. The study also suggested papeda’s polyphyly, in addition to Citrus hongheensis being a possible progenitor species to Citrus maxima. Lastly, we analyzed nucellar embryony (apomixis), an important trait in citrus because it significantly influences strategies for both scion and rootstock breeding. Some of the seedlings arising from a seed of a genotype with nucellar embryony are genetically identical to the seed parent. To better understand the genetic basis of nucellar embryony, a genome-wide association study (GWAS) was conducted separately in Citrus and Poncirus for two distinct but related traits, nucellar embryony and polyembryony. In this study, an average of 46 germinated seedlings from each of 209 accessions were genotyped with KASP SNP markers to determine whether they originated from a nucellar or a zygotic embryo. Using a high density SNP array for citrus to genotype the seed source trees, the GWAS analysis identified a major dominant locus in Citrus and a separate locus in Poncirus.