Except for a group I intron in trnL-uaa occuring in eubacteria and plastids, group I introns are rarely documented in plastid genomes. Here, we report that a green alga, Caulerpa sertularioides, contains three group IA3 introns in the 16S gene (cpSSU), CS-cpSSU.i1, CS-cpSSU.i2 and CS-cpSSU.i3. Each intron has an open reading frame with LAGLIDADG motifs. CS-cpSSU.i1orf and CS-cpSSU.i3orf occur at Loop 6 in the intron secondary structure and CScpSSU. i2orf at Loop 8. CS-cpSSU.i1orf and CS-cpSSU.i2orf contain both LAGLI-DADG motifs but CS-cpSSU.i3orf has only one. CS-cpSSU.i1 and CS-cpSSU.i2 share the insetion sites and the ORFs at Loop 6 and 8 with CpSSU·1 and CpSSU·2 introns of Chlamydomonas pallidostigmatica (Chlorophyceae). In contrast, CS-cpSSU.i3, containing 28 copies of GAAATAT at Loop 6, is a novel intron found only in Caulerpa sertularioides. Possible scenarios of the evolution of the three introns and their possible use in systematic research are discussed.