As reflectance measured via remote sensing is connected to plant light use and morpho-structural features, it can be used to derive spectral proxies of functional traits, or spectro-functional traits. Focusing on disentangling intraspecific trait variability in nature, we evaluated the links between haplotype and spectrofunctional traits in Phragmites australis populations.Haplotypes sequencing and multi-seasonal satellite data were used to evaluate the temporal dynamics of spectro-functional traits for reed stands sampled from seven wetlands in Central Italy, investigating meteoclimatic drivers, the differences across ecological statuses, sites, and haplotypes, and quantifying intraspecific variability due to haplotype or phenotypic plasticity.Five haplotypes were identified, including an unedited one, which explained a substantial portion of intraspecific variability in canopy traits, differing for aquatic and terrestrial stands. We found that meteoclimatic factors impact on aquatic reeds traits (not over terrestrial ones) and a dualism between most and less common haplotypes, pointing to different evolutionary strategies. Dynamics in reed canopy traits were linked to ecological status, site and haplotype, with signs of haplotype-variable effects of dieback on aquatic stands.Evaluating the spectro-functional variability over reed haplotypes may provide a straightforward approach for monitoring the genotype-phenotype relations across scales and assessing their ecological drivers.