The eukaryotic supergroup chromalveolates, as defined in the chromalveolate hypothesis, comprise the chromists (haptophytes, heterokonts and cryptophytes) and the alveolates (dinoflagellates, ciliates and apicomplexa). The assumed chromalveolate monophyly manifested in the chromalveolate hypothesis is deduced from a particular model of plastid evolution, stating that the chromalveolate plastid originated from a single secondary endosymbiotic event where a red plastid was acquired in the common ancestor of all chromalveolates. However, the extraordinary plastid diversity found in one of the chromalveolate lineages, namely the dinoflagellates, reflect a even more complex history of plastid evolution, including evolutionary processes such as tertiary endosymbiosis, kleptoplastidy (i.e. temporarily uptakes of plastids), plastid loss and plastid replacements. This makes the dinoflagellates an ideal group for investigations of plastid evolution in general.In this study, the evolutionary history of chromalveolates is addressed by two approaches, namely investigations of plastid evolution by investigating chloroplast replacement events in dinoflagellates, as well as analyzing the phylogeny of the potential deep-branching chromalveolate lineage Telonema for further understanding of the early evolution and putative monophyly of the group. cDNA libraries from two aberrantly pigmented dinoflagellates were constructed for investigation of the expressed genome, and PCR-amplification, sequencing and subsequent single-gene and concatenated phylogenetic analyses were carried out using nuclear encoded genes that have been shown to be useful for phylogenetic inference of eukaryotes. These analyses indicated that the haptophyte- and prasinophyte-derived plastids found in the aberrantly pigmented dinoflagellates were each acquired only once, replacing the ancestral peridinin plastid. The lineage Telonema was further established as a deep, diverging eukaryotic lineage, possibly associated with the chromalveolates, by combining phylogenetic inference of gene sequences and morphological traits. However, as seen in other phylogenetic studies of this group, the putative monophyly of the chromalveolates were not shown.