Lake Malawi cichlid fish went through a recent adaptive radiation event, which generated more than 500 closely related species in less than 200,000 years. With similar genomic background, the fishes differ dramatically in appearance and behaviour. As such they provide a superb system to study the molecular basis of speciation. Recent work on comparative genomics undertaken at the WT Sanger Institute is in the process of revealing regions under strong selection in the genomes. However, the high degree of morphological difference indicates additional selection possibly on other levels than the genome, e.g. the transcriptome. To test this hypothesis, we plan to compare the total RNA profile of different species of Malawi cichlid fishes, to identify the genes with highest difference of expression level, and put them into context with the morphological and behavioural comparison. To facilitate the analysis we also aim to assemble a reference transcriptome for one of the species, Astatotilapia calliptera. We envisage that the results from this study will serve as the missing puzzle between the genomic analysis and morphological measurement. To this aim, we need the support from the WTSI for the total RNA sequencing. The subsequent data analysis will be performed by visiting workers from the Miska group with the computational resources of the WTSI.