<p>In most plants and algae, chloroplast genomes (cpDNA) generally contain a large inverted repeat (IR) region that separates two single-copy regions. However, as one of the ancient secondary endosymbiotic eukaryotes, Rhodophyta (red algae) chloroplast genomes exhibit great variations in the IR region, and the phylogenetic relationships among the orders in the largest subclass, Rhodymeniophycidae, of Rhodophyta remain elusive. Here, we used 107 completed chloroplast genomes, representing 34 orders and all seven classes of Rhodophyta, to reconstruct the phylogenetic relationships and further reveal the variations and evolutionary pattern of the IR region in the chloroplast genomes. Chloroplast phylogenomic analyses revealed well-supported relationships at the order level in Rhodymeniophycidae. Moreover, we detected four types of variation in chloroplast genomes: IR-presence, IR-absence, IR-aberrance and direct repeats (DRs). The ancestral character reconstruction revealed that IR-absence appeared to be the ancestral state of Rhodophyta, and the IR variations exhibited a trend of “absence–aberrance–presence–absence–direct repeats–absence–presence” over the path of evolution in Rhodophyta. Our study reveals the considerable diversity of chloroplast genomes in Rhodophyta and provides insights into the evolutionary path of the IR in Rhodophyta.</p>