Recognition and delimitation of taxonomic categories of biological organisms are still challenging and full of controversy. We used Ischnosiphon as a model to unravel the importance of morphometrics as individual-based variables to disentangle the morphological variability of plant species. Ischnosiphon spp. continue to be problematic for users, taxonomists and ecologists, due mainly to the huge morphological variability, the species criteria and circumscription proposed for many taxa and the many habitat and vegetative macro-morphological characters lacking in most currently available exsiccates. Twenty-three morphometric variables were sampled from 228 individuals, belonging to 22 Ischnosiphon spp. Principal components and discriminant multivariate analyses were used to describe and identify patterns of morphological variation in Ischnosiphon. Individual-landmark assessment analysed with multivariate methods captured morphometric intraspecific diversity and morphological variability in Ischnosiphon spp., along with the continuous variation of important morphological traits. By examining the morphology of Ischnosiphon spp. through individual-landmark assessment, we demonstrate that different morphological species concepts used today in the identification of the species are difficult to apply. We propose a replicable and analytical framework to accommodate individual variability in species diagnosis in morphologically diverse plant groups.