Recent advances in the field of deep learning have led to a growing interest in the development of NLP approaches for low-resource and endangered languages. Nevertheless, relatively little research, related to NLP, has been conducted on indigenous languages. These languages are considered to be filled with complexities and challenges that make their study incredibly difficult in the NLP and AI fields. This paper focuses on the morphological segmentation of indigenous languages, an extremely challenging task because of polysynthesis, dialectal variations with rich morpho-phonemics, misspellings and resource-limited scenario issues. The proposed approach, towards a morphological segmentation of Innu-Aimun, an extremely low-resource indigenous language of Canada, is based on deep learning. Experiments and evaluations have shown promising results, compared to state-of-the-art rule-based and unsupervised approaches.