Species of Lobophora (Dictyotales) are distributed throughout the sub-tropical and tropical seas worldwide. Recent analyses have revealed high species diversity in regions previously presumed to host only a single species, such as the Bismarck Sea, Eastern Pacific, Western Atlantic, Mediterranean Sea, and Greater Caribbean. Here, samples from Veracruz and Quintana Roo, Mexico, were collected, and 2 genetic markers (cox3 and psbA) were sequenced. The results confirmed the presence of L. dispersa and L. variegata. Lobophora dispersa is recorded for the first time on the Mexican coast. The distribution of its cox3 haplotypes shows genetic differentiation within the Greater Caribbean and Gulf of Mexico, possibly indicating limited dispersal and isolation by distance. Lobophora variegata exhibits lower genetic variability compared to L. dispersa, but its haplotypes did not show any obvious pattern. Lobophora declerckii, previously reported in the “Anegada de Afuera” reef, Veracruz, was not found, possibly due to its affinity to subtidal depths. Morphologically, L. dispersa and L. variegata align with previous descriptions, although we observed more variation in thallus cell thickness in L. dispersa. However, relying solely on morphological characters is insufficient to confidently identify the species, necessitating further sampling to determine the species diversity in Mexico.