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The deep sea is the most extensive habitat on our planet, and it supports surprisingly high biodiversity. With a multitude of different environments and conditions previously thought to be inhabitable, it is unclear how such high diversity was able to develop, but habitat heterogeneity and nutrient flux are certainly important factors to consider. In this review, the different methodologies used to examine biodiversity in the remote depths of the oceans are considered. In addition, the different environments in which biodiversity is studied are presented, and the various hypotheses on how high biodiversity is possible are examined. Unfortunately, this diversity is threatened by human impact similarly to shallow waters, and future endeavors such as deep-sea mineral extraction must be considered as a major threat to the environment. Many mysteries persist in the deep sea, but it is certain that threats such as overfishing, plastic pollution, and changes in ocean chemistry due to climate change are impacting even the most remote places in the oceans. It remains uncertain whether the deep sea is resilient toward anthropogenic disturbances, yet this is difficult to research on short timescales. There is little hope for areas in which exploitation, such as deep-sea mining, will be directly impacting the benthos and proper regulations are required to preserve biodiversity in the deep sea.

Correct identification of species is required to assess and understand the biodiversity of an ecosystem. In the deep sea, however, this is only possible to a limited extent, as a large part of the fauna is undescribed and the identification keys for most taxa are inadequate or missing. With the progressive impact of climate change and anthropogenic activities on deep-sea ecosystems, it is imperative to define reliable methods for robust species identification. In this study, different techniques for the identification of deep-sea species are tested, including a combination of morphological, molecular (DNA barcoding, and proteomic fingerprinting), biogeographical and ecological modeling approaches. These are applied to a family of isopods, the Haploniscidae, from deep waters around Iceland. The construction of interactive identification keys based on the DELTA format (DEscription Language for TAxonomy) were a major pillar of this study, the evaluation of which was underpinned by the application of the supplementary methods. Overall, interactive keys have been very reliable in identifying species within the Haploniscidae. Especially in a deep-sea context, these types of keys could become established because they are easy to adapt and flexible enough to accommodate newly described species. Remarkably, in this study, the interactive key enabled identification of a supposedly new species within the Haploniscidae that was later verified using both molecular genetic – and proteomic methods. However, these keys are limited given that they are based on purely morphological characteristics, including where species with strong ontogenetic or sexual dimorphism occur as both genders are not always described. In this case, integrative taxonomy is the method of choice and the combination presented here has been shown to be very promising for correct identification of deep-sea isopods.