Madagascar, renowned for its unique biodiversity, faces significant environmental threats. Despite their vital ecosystem services, invertebrates, such as Lepidoptera, remain understudied, especially within the Malagasy Island. Indeed, butterflies and moths often serve as biodiversity indicators. This study investigates lepidopteran community structure across different habitat types: protected areas and anthropized areas, represented by forest edges and agroforestry through four expeditions to Madagascar’s moist eastern forests. Both sampling methods were employed including butterfly nets and fermented fruit-baited traps. While nets accounted for 90% of captures, highlighting operator bias, bait traps captured unique species, emphasizing the complementarity of these methods. With over 891 captured specimens, 418 macrolepidopterans were identified at the species level for a total of 50 species. Protected forests hosted 80% of endemic Lepidoptera reliant on specialized ecological niches, while anthropized zones were dominated by common generalist species which are resilient to habitat changes. While the species richness and composition of sampled microlepidoptera are similar, habitat fragmentation created diverse environmental conditions, hosting specific populations. Conservation challenges persist, particularly for endemic species vulnerable to poaching. It is crucial to continue sampling Madagascar’s lepidofauna, as this offers considerable potential for the sustainable maintenance of ecosystems and the long-term preservation of biodiversity of the Malagasy Island.