The brown macroalgal genus Lobophora plays important ecological roles in many marine ecosystems. This group has received much attention over the past decade, and a considerable number of new species have been identified globally. However, our knowledge of the genus diversity and ecology along south-east Asian coasts are still limited. Given the growing body of research that uses a combination of molecular and morphological data to identify cryptic species, this study investigates the diversity of Lobophora in the western Gulf of Thailand using morphological and molecular data, as well as their interactions with scleractinian corals. A total of 36 Lobophora specimens were collected from 15 sites in the western Gulf of Thailand and used for molecular and morphological analyses. One mitochondrial (cox3) and two chloroplast (psbA and rbcL) genes were amplified and sequenced for molecular phylogenetic analyses. Based primarily on phylogenetic evidence, two new species were formally described, L. chumphonensis sp. nov. and L. thailandensis sp. nov. Additionally, L. lamourouxii was newly recorded from Thailand. Two new lineages of Lobophora obscura were identified, L. obscura12 and L. obscura13. Among the Lobophora species identified, three were found in interaction with corals, the most notable of which was the massive coral Porites. Lobophora chumphonensis sp. nov. only interacted with Porites by growing on bare coral skeleton between Porites colonies. Furthermore, L. obscura13 was observed under the branching coral Pocillopora. Our findings revealed that Lobophora presented both effects and absence of effects on coral. A thorough understanding of Lobophora diversity and ecology is essential for ongoing and future research on coral–macroalgal ecological relationships.