In order to understand the epidemiology of this avian malaria infections both geographically and across host species there is a need of more polymorphic markers and knowledge about genes expressed during the infection of the host. However, technical difficulties have hindered the development of such molecular markers. The main difficulty is the fact that the host (birds) has nucleated erythrocytes and there is a 52-fold difference in the genome size between the host and the parasite. This has caused problems in trying to isolate and amplify novel nuclear genes of the avian malaria parasites. In order to overcome this difficulty and gain molecular data on nuclear genes we have sequenced blood transcriptomes of common crossbills experimentally infected with Plasmodium relictum SGS1 lineage. During development in the blood, the parasite undergoes several cycles of asexual development (erythrocytic merogony) and is invading numerous host cells and thus is expected to have a high level of gene expression. This data will serve as a resource for researchers interested in developing more molecular markers and investigating genes expressed during the erythrocytic development of avian malaria parasite. With this data we hope to take the first step into the understanding of the mechanism behind the exhibited host generalism as well as understanding how different avian malaria lineages have spread around the globe.