Horticultural crops and their wild relatives showed large plastid and mitochondrial DNAs diversity in the last decade, especially with the development of advanced molecular techniques such as Barcoding and Next-Generation Sequencing (NGS). In the global market there are plenty of unidentified plants which are being sold without paying intellectual propriety rights, Barcoding will enable us to monitor this trade and eliminate illegal operations. Medicinal plants represent an important part of horticultural crops and both of producing and consuming countries lack an effective tool of species identification and herbal product authentication. Several successful attempts were made on the field of application of barcoding in species identification of medicinal plant and consumer protection through standardizing food safety measure. The applications of next-generation sequencing in the fields of organellar genome studies in horticultural crops, flora and fauna have assessed in the sequencing of more than 100 plastomes and 70 mitochondrial genomes of angiosperms. In this book I tackle hard issues bout horticultural crops diversity and their studies by barcoding and NGS.