Brown algae, a group of heterokont protists, exhibit complex multicellularity and diverse gamete types. This study establishes their phylogeny and evolutionary timeline using plastid genomes, revealing that brown algae originated during the late Ordovician Period (ca. 450 Ma), coinciding with a major diversification of marine fauna. Major diversification and gamete type transitions occurred during the Mesozoic Era. Isogamy reappearances correlate with gametic parthenogenesis. The study analyzed 138 plastid genomes, including 35 new brown algal plastid genomes, to clarify the diversification within the brown algal crown radiation (BACR) clade. The results show that brown algae first evolved true multicellularity with plasmodesmata and reproductive cell differentiation during the late Ordovician. The diversification of major brown algal orders accelerated during the Mesozoic, coinciding with Pangea rifting and diversification of other heterokont algae. The transition from ancestral isogamy to oogamy was followed by three simultaneous reappearances of isogamy during the Cretaceous. These are concordant with a positive character correlation between parthenogenesis and isogamy. The study provides a new timeline for brown algal evolution, combined with knowledge of past environmental conditions, shedding new light on their diversification and the intertwined evolution of multicellularity and sexual reproduction. The results suggest that brown algae evolved complex multicellularity with plasmodesmata and reproductive cell differentiation during the late Ordovician, and their diversification accelerated during the Mesozoic. The study also shows that isogamy reappearances correlate with gametic parthenogenesis, and that the transition from isogamy to oogamy was followed by three simultaneous reappearances of isogamy during the Cretaceous. The findings highlight the importance of understanding the evolutionary processes behind these transitions.Brown algae, a group of heterokont protists, exhibit complex multicellularity and diverse gamete types. This study establishes their phylogeny and evolutionary timeline using plastid genomes, revealing that brown algae originated during the late Ordovician Period (ca. 450 Ma), coinciding with a major diversification of marine fauna. Major diversification and gamete type transitions occurred during the Mesozoic Era. Isogamy reappearances correlate with gametic parthenogenesis. The study analyzed 138 plastid genomes, including 35 new brown algal plastid genomes, to clarify the diversification within the brown algal crown radiation (BACR) clade. The results show that brown algae first evolved true multicellularity with plasmodesmata and reproductive cell differentiation during the late Ordovician. The diversification of major brown algal orders accelerated during the Mesozoic, coinciding with Pangea rifting and diversification of other heterokont algae. The transition from ancestral isogamy to oogamy was followed by three simultaneous reappearances of isogamy during the Cretaceous. These are concordant with a positive character correlation between parthenogenesis and isogamy. The study provides a new timeline for brown algal evolution, combined with knowledge of past environmental conditions, shedding new light on their diversification and the intertwined evolution of multicellularity and sexual reproduction. The results suggest that brown algae evolved complex multicellularity with plasmodesmata and reproductive cell differentiation during the late Ordovician, and their diversification accelerated during the Mesozoic. The study also shows that isogamy reappearances correlate with gametic parthenogenesis, and that the transition from isogamy to oogamy was followed by three simultaneous reappearances of isogamy during the Cretaceous. The findings highlight the importance of understanding the evolutionary processes behind these transitions.