Abstract Living beings inhabit heterogeneous environments, in which communities that are classified as discrete can be continuous and connected in innumerable ways. The components of food webs can cross borders between ecosystems, and as result, the structure and trophic dynamics of ecosystems can change. The goal of this study was to evaluate trophic connectivity between the terrestrial and marine ecosystems of Malpelo Island, Colombia (4º00’05.63” N; 81º36’36.41” W), based on the isotopic (δ 13 C and δ 15 N) assessment of 403 samples (107 terrestrial and 296 marine). Samples were collected in 2017–2021. δ 13 C Terrestrial values ranged from − 30.3‰ to − 15.0‰ and δ 13 C Marine ranged from − 24.0‰ to − 9.8‰; δ 15 N Terrestrial ranged from 3.7‰ to 21.3‰ and δ 15 N Marine ranged from 4.5 to 16.9‰. The mixing model (simmr package) indicated that detritus Terrestrial (δ 13 C = − 18.9 ± 0.30‰ SE) contributed more to the food web than C 3 plants (–29.4 ± 0.22‰), and reflected high δ 13 C Marine content. There was high isotopic overlap (65–82%) and a high trophic connection between environments of Malpelo Island due to high similarity between isospaces. These results evidence the role of the donor habitat (marine) on the receptor habitat (terrestrial) and the role of the Nazca booby Sula granti regarding nutrient transfers between the two environments. The presence and preservation of this seabird is essential to maintain the balance of this insular ecosystem. The analysis of δ 13 C and δ 15 N tracers was useful to establish the trophic relationships between small oceanic island environments with presence of large seabird communities.