Deep-sea chondrichthyans are cryptic species subject to increasing anthropogenic exploitation. Defining their role in deep-water ecosystems is therefore crucial for predicting the ecosystem-wide effects of their removal. Stable isotope analyses (SIA) of carbon and nitrogen have been increasingly used in chondrichthyan studies as a non-lethal method to investigate aspects of their ecology. In recent years these methods have been applied to deep-sea chondricthyans to investigate their trophic structure, niche width, and describe energy flow in the deep sea. Despite the increasing popularity of SIA in deep-sea chondrichthyan studies, methods rely on a multitude of assumptions, such as the need to determine accurate trophic discrimination and tissue turnover rates, which are currently lacking for most species. These uncertainties may preclude the reliability of isotope-based approaches, and as a result inferences from isotopic data must be viewed with relative caution. Due to the growing use of isotopic-based approaches in deep-sea chondrichthyans, we review the literature in the context of current methodological challenges and ecological inferences. We provide recommendations and novel approaches that may help develop and refine a rapidly growing field of study.