We review current knowledge of cyanobacterial diversity and abundance in New Zealand's indigenous tussock grassland soils and present preliminary results on microbial diversity in grassland soils. A cyanobacterial community of eight operational taxonomic units was present in soil samples from Deep Stream indigenous grassland. This included strains belonging to the orders Chroococcales, Oscillatoriales and Nostocales. UniFrac analysis showed that the cyanobacterial populations were significantly different between burnt and unburnt soils. In addition, we outline the different techniques used to investigate cyanobacterial diversity and the role of cyanobacteria in providing fixed nitrogen into terrestrial ecosystems. Approaches include classical techniques of isolating cyanobacteria on selective media as well as traditional culture-independent methods involving DNA fingerprinting and/or analysis of molecular markers, including the use of polymerase chain reaction amplification in combination with Sanger sequencing to assess phylogenetic diversity in ecosystems. These labour intensive approaches are often limited by the number of samples that can be analysed. Advances in microarrays and highthroughput sequencing technologies now enable in-depth analysis at a lower cost and allow variations in microbial communities to be detected at different taxonomic levels. We compare the advantages and limitations of both traditional and new approaches.