After introducing the platforms, applications and advances in next generation sequencing technologies the author will discuss his involvement with several genome sequencing initiatives, focusing more closely on the tammar wallaby genome project. The Baylor College of Medicine, Australian Government and University of Connecticut teamed together (under the KanGO consortium) as part of an international effort to generate a de novo genome sequence for the marsupial model species, the tammar wallaby (Macropus eugenii). The work involved assembling this 2.7 GB mammalian genome from sequence produced from Sanger sequencing reads (Baylor and RJKEN), Illumina sequencing reads (Australian Genome Research Foundation, AGRF), and 454 reads (AGRF and the CAGT at UConn) using unique assembly tools developed. The genome sequencing initiative for the tammar wallaby has also afforded an opportunity to explore the evolution of repeat classes as well as each of the major classes of small RNAs, siRNAs, miRNAs, piRNAs, and the newest class of small RNAs, crasiRNAs (centromere repeat associated short interacting RNAs), first discovered in the tammar wallaby. Although only recently discovered, small RNAs have proven to be essential regulatory molecules encoded within eukaryotic genomes. The analysis includes the detailed examination of these small RNAs, salient features that define their canonical members and the constitution of species-specific members derived from mobile genetic elements. Understanding the evolution of these important regulators and surveyors of the genome in this unique marsupial model brings valuable insights to the community of small RNA researchers.