A joint GARNet-Genetics Society meeting on “New Technologies to Advance Plant Research”, held in November 2012 at Liverpool University, was the catalyst for this special Thematic Series on Next Generation Sequencing Technologies for Plant Research. Next-generation sequencing (NGS) encompasses a number of different sequencing technologies (e.g. Illumina/Solexa, Roche 454, Ion torrent and SOLiD sequencing) that share the feature of allowing us to sequence DNA and RNA much more quickly and cheaply than Sanger sequencing. These new massively parallel sequencing technologies are revolutionising molecular biology by providing insights into the genome, the transcriptome and the epigenome on an unprecedented scale. The thematic series aims to cover all aspects of the application of new sequencing technologies to plant research - and new submissions (including Methodology papers) will be encouraged until 31st December 2013.