In 1990, a Nordic group, "Projektstyregruppen for Fiskeimmunologi" was founded within the framework of the Nordic Council of Ministers and given the task to enhance cooperation between the Nordic countries in the field of fish immunology. The initiative and funding came from Nordisk Programkomité for Bioteknologi, NPB. Torger Börresen was appointed to coordinate the initiation of the immunology group with the aim of making the researchers in all Nordic countries work together to reduce diseases in aquaculture. 

The first meeting of the immunology group was held in Copenhagen in 1990 and the representatives were, Torger Börresen and Claus Koch from Denmark, Sinikka Pelkonen from Finland, Sigridur Gudmundsdottir from Iceland, Trond Jörgensen from Norway and Lars Pilström from Sweden. During the next 3 years, the period for which funds were granted from the Nordic Council of Ministers, the main activities of the group were 1) to give mobilization grants to scientists in the field, 2) a project for the making of monoclonal antibodies against antigens on cells from the immune system of rainbow trout and 3) the organization of two international conferences. The first one was held in Tromsö, Norway in 1991 and the second in Lysekil, Sweden in 1993. Since then meetings have been held in Reykjavik (1995), Hirtshals (1998), Oslo (2001), Finland (2004), and Scotland (2007). 

At the 5th meeting of the immunology group in November 1992, the collaboration initiated between the laboratories in the Nordic countries seemed to be so successful, and the international appreciation of the conferences were so pronounced, that it was decided to try to find a way to continue with the cooperation although the money allocated by NPB was running out. The group proposed to form an independent society. That was formally done during the symposium in Lysekil, where the official inaugural assembly of the representatives took place, and a board was elected. The board members elected were the same people as mentioned above, with Lars Pilström being the first chairman. Bylaws for the society were also adopted at this occasion. The organization continued to be Nordic in the sense that the board members have been elected from Nordic countries but the membership is open to anyone. Also, grants from the Nordic Council of Ministers and from local Nordic funds were applied for and obtained, and have been allocated to NOFFI for special tasks. 

The general assembly in 2001 decided to use the time until the general assembly in 2004 to discuss possibilities concerning election of the board in the future, i.e. whether or what changes might be needed concerning the organization.The main activities of "Projektstyregruppen for Fiskeimmunologi", and later NOFFI, have been arrangements of symposia, initiation of collaboration projects and the issuing of mobilisation grants for young researchers.

In 2007 the society decided to change its name to European Organisation of Fish Immunology (EOFFI) reflecting a change over the years of the society having extended its activites beyond the Nordic sphere. The change will result in the meetings being held outside the Nordic countries. We started in 2007 in Scotland and the 1st meeting of EOFFI was held in 2010 in Viterbo, Italy. 

And in Viterbo in 2010 it was decided to establish a new, joint international society of fish and shellfish immunology. The first international Conference of the society was held in Vigo in 2013 and 2nd conference in Maine 2016. This was followed by the conference in Gran Canaria 2019.