Notothenioids are the most abundant group of teleost fish found in the Southern Ocean. These fish evolved relatively recently from a single benthic ancestor and radiated and expanded in the extreme cold of Antarctica waters and their physiology was adapted accordingly. Surprisingly, little is known about their immune system and how immune defences were modulated during adaptation to the cold environment and to its water specific microbiome. The main objective of this thesis was to characterise the immune cellular and humoral responses to bacterial and viral-like challenges in immune tissues and plasma of two phylogenetically related notothenioids, Notothenia coriiceps and Notothenia rossii. The methodologies applied were based on DNA sequencing technologies and biochemical assays to measure functional plasma enzyme activity using a comparative approach. This study a) characterised and uncovered a role of iron-metabolism and of the pattern recognition receptors family toll-like receptors (TLRs) after a LPS immune challenge, b) characterised for the first time the transcriptomes of important immune tissues (head-kidney, skin, duodenum, liver and spleen) and their response to bacterial and viral challenges and in response to temperature, c) described the microbiome communities associated to important immune tissue barriers in recently caught and immune challenged notothenioids. The results contribute substantially to the understanding of the main immune and non-immune pathways in the defence against external agents in Antarctic notothenioids.