Eukaryotic cells internalize cargos specifically through clathrin-mediated endocytosis (CME) or clathrin-independent endocytosis (CIE). EndophilinA2 was shown as preferentially implicated in CIE, although initially involved in CME. Here, we investigated the native interplay of endophilinA2 and dynamin2 during CME as compared to CIE. We developed an unbiased integrative approach based on genome engineering, robust tracking methodology, and advanced analytics. We statistically identified CME and CIE subpopulations corresponding to abortive, active, and static endocytic events. Depletion of dynamin2 strongly affected active CME and CIE events, whereas the absence of endophilinA2 impacted only CIE. Accordingly, we demonstrated that endophilinA2 is needed for dynamin2 recruitment during CIE, but not in CME. Despite these differences, endophilinA2 and dynamin2 acted at the latest stage of endocytosis within a similar stoichiometry in both mechanisms. Thus, we propose a conserved function of dynamin2 and endophilinA2 in vesicle scission, but a differential regulation of their recruitment during CME and CIE. Display omitted •Native dynamics of endophilinA2 and dynamin2 followed in CME and CIE•Analytics of subpopulation dynamics reveal similarities between CME and CIE•Dynamin2:endophilinA2 stoichiometry is conserved between CME and CIE•EndophilinA2 is essential for dynamin2 recruitment only in CIE Bertot et al. interrogate endophilinA2 dynamics and interplay with dynamin2 in clathrin-mediated (CME) and -independent (CIE) endocytosis. The work shows that endophilinA2 is a conserved endocytic factor in both pathways, acting with dynamin in a similar stoichiometry, but its presence is required only in CIE for dynamin2 recruitment.