Chondracanthus chamissoi is part of the diet of coastal people from Peru and is exported dehydrated to Asian countries for direct consumption. Although it is considered endemic to Peru and Chile, its range has extended to distant regions, such as Korea, Japan, and France. Using morphological and molecular approaches, we examined specimens from Peru assigned to C. chamissoi (including the taxon of uncertain status Chondracanthus glomeratus) to improve phylogenetic and geographical information and characterize its morphological variability. Twenty-one localities on the Peruvian coast were sampled, obtaining 102 COI and 27 rbcL sequences. To differentiate both entities, morphological characters such as thallus size, consistency, arrangement of main and secondary axes, branching patterns and location of reproductive structures, were analyzed on 46 specimens. While morphological characteristics are clearly contrasting among the two groups, both COI and rbcL phylogenies revealed a well-supported clade with no genetic differentiation between the two morphologies. Therefore, the phylogenies indicate that C. chamissoi and C. glomeratus form a single taxonomic entity with high morphological variability, large geographic distribution and at least two morphological forms. The smaller form of C. chamissoi can be identified as C. chamissoi f. glomeratus. Such morphological variability can be of interest for future aquaculture development.