Tisochrysis lutea is a haptophyte microalga important in aquaculture. The 105,837-bp chloroplast genome encodes 113 proteins, 27 different transfer-RNAs and ribosomal-RNAs. Phylogenetic analysis on currently available chloroplast sequences showed T. lutea was most closely related to Emiliania huxleyi. Unlike E. huxleyi chloroplast DNA, T. lutea contains directly-repeated ribosomal repeats following multiple genome rearrangements during evolution. The non-identical 4.9-kb ribosomal direct-repeats are distinguished by 42 nucleotide polymorphisms and three single- or double-nucleotide INDELs. This is unlike land plant and green algal chloroplast genomes in which efficient copy correction by homologous recombination ensures identical long inverted repeats containing the rRNA operons. Imperfect rDNA repeats are also found in the chloroplast genomes of cryptophytes, rhodophytes and other haptophytes. Reduced copy correction rates in these algal lineages raise questions on the mechanism(s) by which genetic uniformity of multi-copy chloroplast genomes is maintained and has implications for developing chloroplast transformation in these species.