The Anthropocene has had deteriorating effects on global biodiversity, and we are navigating our days amid a sixth mass extinction era. An excessive loss of biodiversity is a particular concern for oceans due to the huge uncharted geographic ranges, the complex and tremendously unexplored taxonomy of marine species, and vast variety of marine ecosystem services. Marine mammals, specifically cetaceans are important ecosystem engineers and indicator species of ocean health, therefore it is alarming that 37 % of know species are categorized as conservation concern (critically endangered, endangered, vulnerable or near threatened). These numbers are striking but not surprising since cetaceans are subjected to multiple anthropogenic stressors, most prominently pollution, ocean noise and climate change, which affect their habitats, life histories, fitness and survival. Due to the elusive nature of cetaceans and the long list of challenges associated with marine mammal surveys, there are major knowledge and data gaps about the habitat, abundance and distribution of many species globally. There is a dire need to develop and implement state-of-the art survey methods to overcome the elusiveness of cetaceans and unravel the unseen and unheard in the underwater realm. Environmental DNA (eDNA) emerged as tool for aquatic biodiversity and answered several questions asked about rare, elusive or cryptic species that are difficult to survey with traditional methods. However, several questions related to the applications of eDNA methods to cetacean species have not even been asked prior to this work, and I aimed to address as many as possible in the scope of three years. In this work I summed up these questions and answers in four main chapters, and aspired to highlight the recent advances, applications and challenges studying cetaceans with eDNA.