Next-generation sequencing (NGS) technologies are a powerful new tool for conducting studies in ecology and evolutionary biology. NGS offers the possibility of genetic characterisation of many loci in non-model organisms, opening up a plethora of research opportunities unimaginable 10 years ago. This was the motivation behind a discussion meeting entitled Next generation plant ecology and evolution, held at the Royal Botanic Garden Edinburgh in October 2011. This special feature includes a series of papers presented at the meeting. These studies demonstrate the wide range of areas on which the use of NGS can shed light, ranging from the characterisation of single loci to whole genomes.