After more than 250 years of trying, we still do not know the number of animal species on our planet. However, we do know that a large proportion of the unknown species are arthropods and live in the tropics. In this thesis, I explore new ways to utilize Next Generation Sequencing (NGS) technologies for fast and large-scale species discovery. I first test the performance of mini-barcodes for distance-based species delimitation and compare the performance to tree-based species delimitation. After evaluating these techniques, I utilize NGS barcodes to demonstrate that they can be used to rapidly pre-sort specimens into putative species regardless of life history stage. I then use NGS barcodes to document that mangroves are home to a previously overlooked large and distinct insect fauna. Lastly, I evaluate three different techniques for obtaining mitochondrial genomes and nuclear sequences for building species-rich trees: mitochondrial metagenomics, multiplexed tagged amplicon sequencing and hybrid enrichment.