Capsaspora owczarzaki, a protistan symbiont of the pulmonate snail Biomphalaria glabrata, is the centre of much interest in evolutionary biology due to its close relationship toMetazoa. Thewhole genome sequence of this protist has revealednewinsights into the ancestral genome composition of Metazoa, in particular with regard to gene families involved in the evolution ofmulticellularity. The draft genome revealed the presence of 23 families of transposable element,made up from DNA transposon as well as long terminal repeat (LTR) and non-LTR retrotransposon families. The phylogenetic analyses presented here show that all of the transposable elements identified in the C. owczarzaki genome have orthologous families inMetazoa, indicating that the ancestralmetazoan also had a rich diversity of elements. Molecular evolutionary analyses also showthat the majority of families has recently been active within the Capsaspora genome.One familynowappears to be inactive and a further five families showno evidence of current transposition. Most individual element copies are evolutionarily young; however, a small proportion of inserts appear to have persisted for longer in thegenome.Thefamiliespresent in thegenomeshowcontrastingpopulationhistories and appear to be in different stages of their life cycles. Transcriptome data have been analyzed frommultiple stages in the C. owczarzaki life cycle. Expression levels vary greatly both between families and between different stages of the life cycle, suggesting an unexpectedly complex level of transposable element regulation in a single celled organism.