Epiphyton might have distinctive influence on the morphology of substrate macrophyte. In this article, we evaluate the influence of epiphyton on the morphological characteristics of their substrate submerged macrophyte, Potamogeton perfoliatus under two light intensities. The experiment was carried out for a period of 84 days in 12 glass aquaria under laboratory conditions. It was based on a 2 × 2 factorial design with epiphyton status (present or absent) and light intensity (200 or 80 μE m⁻² s⁻¹). Both epiphyton and light intensity had significant effects on the morphology and biomass allocation of the experimental plants. The average number of leaves, total length of newly recruited shoots and diameter of stems were greater in the epiphyton-free control plants than in the epiphyton-colonized plants under low light conditions. The plants with epiphyton allocated more biomass in their rhizomes and roots (% relative to total biomass basis) when compared to the control plants in both light intensities. There were also significant epiphyton–light interactions. The control plants under low light intensity showed higher internodal elongation in their main shoots when compared to the plants under high light intensity as an adaptation mechanism. Whereas the plants with epiphyton did not show such an adaptation. The new shoots of the control plants under low light intensity did not show any internodal elongation as observed in the main shoots. Furthermore, the length of the leaves of main shoots was larger in control plants with epiphyton and high light intensity than in plants with epiphyton and low light intensity, but such a variation was absent in the new shoots. We conclude that the long-term colonization by epiphyton and their shading effects induced the observed morphological changes in plants.