The glaucocystophyte Cyanophora paradoxa contains cyanelles, plastids with prokaroytic features such as a peptidoglycan wall and a central proteinaceous inclusion body. While this central body includes the majority of the enzyme ribulose 1,5-bisphosphate carboxylase/oxgenase Rubisco), the presence of a carbon-concentrating mechanism (CCM) in C. paradoxa has only been hypothesized. Here, we present physiological data in support of a CCM: CO(2) exchange activity as well as apparent affinity against inorganic carbon were found to increase under CO(2)-limiting stress. Further, expressed sequence tags (ESTs) of C. paradoxa were obtained from two cDNA libraries, one from cells grown in high [CO(2)] conditions and one from cells grown under low [CO(2)] conditions. A cDNA microarray platform assembled from 2378 cDNA sequences revealed that 142 genes significantly responded to a shift from high to low [CO(2)]. Trends in gene expression were comparable to those reported for Chlamydomonas reinhardtii and the cyanobacterium Synechocystis 6803, both possessing a CCM. Among genes regulated by [CO(2)], transcripts were identified encoding carbonic anhydrases (CAs), Rubisco activase and a putative bicarbonate transporter in C. paradoxa, likely functionally involved in the CCM. These results and the polyhedric appearance of the central body further support the hypothesis of a unique 'eukaryotic carboxysome' in Cyanophora.