SUMMARYHalimeda macroloba is a common widespread and morphologically variable species in the Indo‐Pacific Ocean. A series of morphometric data (16 morphological and 46 anatomical variables) and the chloroplast‐encoded tuf A gene were examined to explore the morphological and genetic variations within the species and to better determine species boundaries in H. macroloba in Thai waters. Moreover, the environmental conditions, which may affect morphological variations in H. macroloba, especially of Haplotype I were examined. Our results showed that H. macroloba has more morpho‐anatomical variability and broader species boundaries than previously thought in several characters: holdfast type, segment shape and size, node height with differences in pore size, the presence of two additional patterns of peripheral utricle as seen in surface view, and additional layers of utricles (up to seven layers). Additionally, two new variable characteristics have been reported for the first time, i.e. shape and margin of peripheral utricles. Water depth and light correlated with thallus morphology, larger thalli and segments with a greater number of utricle layers were associated with subtidal plants, while smaller thalli and segments were found in the intertidal or high light intensity areas. The high plasticity of this species may explain why in the Indo‐Pacific Ocean this species is common and dominant.