To shed light on chloroplast genome evolution in the phototrophic euglenoids the cpGenomes of Euglena mutabilis (SAG 1224-9b), Trachelomonas grandis (SAG 204.80) and Eutreptiella pomquetensis (CCMP 1491) were isolated, sequenced and annotated. The chloroplast genomes were investigated intensively and compared to other cpGenomes of phototrophic euglenoids, with special focus on genome size and structure, number and localization of rRNA operons as well as introns. As a cause for genome size differences three major reasons have been identified. First, the intergenic space between the cpGenomes of different taxa varied greatly, even between closely related species. Second, the rRNA operon numbers between different taxa were not uniform. Third, the different intron numbers and intron types between different taxa led to the main reason for size differences in euglenoids cpGenomes. Comprehensive trends of intron number and intron type have been detected in closely as well as distantly related euglenoids. These trends can be used to explain intron density and quantity as well as high or low similarities in the evolution of introns in all phototrophic euglenoids. The expansion and evolution of psbC introns can partly be elucidated by assumed horizontal intron transfers in the chloroplast of euglenoids after the split from Eutreptiales and Euglenales. Findings concerning the emergence and evolution of group III introns supported the hypothesis that group III introns are degenerated group II introns. Surprisingly, the cpGenomes of the basally branching Eutreptiales are free of group III introns, although the results indicated that their evolution began in Eutreptiales as intermediate stages of group II and III introns (mini group II introns). Furthermore, a new phylogenomic analysis of phototrophic euglenoids was performed and compared to recently published phylogenetic analyses. As a new approach genome-level characters from all known cpGenomes of euglenoids have been used as a tool to complement the phylogenomic analysis. Metacharacter analyses yielded gene arrangement, cluster arrangement and rRNA operons as viable metacharacters with partly important modifications between the taxa. Significant cluster rearrangement was identified in several clades that matched the phylogenetic reconstruction. Using the rRNA operon as a metacharacter revealed a trend of loss of one rRNA copy following the diversification of Euglenales. Basally branching Eutreptiales contained two copies, which is identical to the structure in the surmised chloroplast donor Pyramimonas parkeae. Only for both Euglena gracilis species and Strombomonas acuminata an independent acquirement of further rRNA operons was recognizable. The cpGenome of Eutreptiella pomquetensis showed the same quadripartite cpGenome structure as Pyramimonas parkeae, corroborating the close relationship between these two taxa. The present work provides a sound basis for further examinations of chloroplast genome analyses to get a more thorough understanding of intron evolution within the phototrophic euglenoids. Likewise it represents a precursor for future studies concerning genome-level features in phototrophic euglenoids.