Transportation plays a pivotal role in the industrial landscape, and the ecotourism sector, particularly sustainable ecotourism, is no exception. Sustainable ecotourism places emphasis on the responsible management of natural resources, aiming to foster comprehension, appreciation, and the conservation of both the environment and cultural heritage. The purpose of this research is to examine how the emergence of logistics transportation studies is driven by the transportation needs of island communities and tourists to increase sustainable ecotourism industry activities. Logistics transportation services that support ecotourism is a relatively new study of existing logistics resources in Indonesia. This study chooses sea transportation routes for the Karimunjawa Islands and Jepara. The logistics services for tourism transportation provided by the government and third parties pay little attention to sea transportation routes that pass-through conservation areas, namely the Panjang Island Conservation Area and Karimun Jawa National Park. Indeed, there has been a sea route provided, but several obstacles arose when passing through the conservation area. The establishment of novel transportation routes emerges as a viable solution for bolstering the sustainable ecotourism sector and addressing the transportation requisites of the local community. Additionally, these new transportation routes can yield positive outcomes for the safeguarding of conservation areas.