Among the brown algal lineages, ectocarpales species have isogamous fertilization in which male and female gametes are morphologically similar. in contrast, female gametes are much larger than male gametes in the oogamous species found in many other brown algal lineages. it has been reported that the plastids of isogamous species are biparentally inherited whereas the plastids of oogamous species are maternally inherited. in contrast, in both isogamous and oogamous species, the mitochondria are usually inherited maternally. to investigate whether there is any relationship between the modes of inheritance and organellar genome architecture, we sequenced six plastid genomes (ptDnA) and two mitochondrial genomes (mtDnA) of isogamous species from the ectocarpales and compared them with previously sequenced organellar genomes. We found that the biparentally inherited ptDnAs of isogamous species presented distinctive structural rearrangements whereas maternally inherited ptDnAs of oogamous species showed no rearrangements. our analysis permits the hypothesis that structural rearrangements in ptDnAs may be a consequence of the mode of inheritance. The brown algae (Phaeophyceae) are a group of photosynthetic heterokonts (=stramenopiles), a secondary endosymbiotic lineage containing red algal-derived plastids 1. The four brown algal orders analyzed in this study, Ectocarpales, Fucales, Laminariales, and Dictyotales, have macroscopic thalli and are distributed worldwide in low-to-mid latitudes where they play important roles in marine ecosystems. Also, they have great potential for commercial uses such as food or in other seaweed industries. From a taxonomic point of view, the orders Ectocarpales, Fucales and Laminariales are grouped into the subclass Fucophycidae, which is defined as a lineage derived from the brown algal crown radiation (BACR), whereas Dictyotales is classified into the Dictyotophycidae 2 (Fig. S1). The life cycles of most brown algae, including species of the Laminariales and Ectocarpales, are characterized by an alternation between a diploid sporophyte and a haploid gametophyte (i.e., a diploid-haploid life cycle). In contrast, in the Fucales meiosis occurs in the parental diploid plants and they directly produce gametes (i.e., a diplontic life cycle) 3,4. Three fertilization types can be defined based on the morphologies and flagella of gametes, independent of whether they are produced via a gametophyte stage or not: the isogamous type in which flagel-lated gametes are morphologically similar; the anisogamous type where one flagellated gamete is larger than the other; and the oogamous type in which one gamete is a non-motile cell called the egg cell (or oocyte) and the other is a smaller, flagellated sperm cell 5. Most brown algae, including the Laminariales and most species of the Fucales, are oogamous. Anisogamy is only observed in a few lineages such as the Onslowiales, Asterocladales, Nemodermatales, and in some Fucales, Sphacelariales and Ectocarpales species. With the exception of the orders Ectocarpales and Sphacelariales, isogamy is observed only in some species-poor orders such as the Ralfsiales, Scytothamnales, Ascoseirales, Syringodermatales and Ishigeales. Most of the 750 Ectocarpales species are considered to be isogamous 1,6 , although some of these species exhibit a very low level of anisogamy, for example the