From its inception, Cephalonia Botanica has been acknowledged by Greek and foreign bodies. It is a member of BGCI (Botanic Gardens Conservation International) and IPEN (International Plant Exchange Network) and has collaborated with large Botanic Gardens in South England. In particular, Cephalonia Botanica collaborates with the Sir Harold Hillier Gardens and Arboretum, sending its personnel for scientific training in the design and implementation of educational programmes for kindergarten and primary school children. Cephalonia Botanica has been exchanging know-how with the Botanical Garden of Wales on issues concerning the organization and management of a newly established Botanic Garden. Finally, in an effort to create a Seed and Bulb Bank for Cephalonia's indigenous plants, Cephalonia Botanica has sought consultation and training from the Millennium Seed Bank located at Wakehurst Place, Sussex.

In Greece, it has collaborated with EKEK TAKI (Centre for Professional Training of the Prefecture of Cephalonia and Ithaca) on environmental and cultural issues. Crucially, it is currently collaborating with N.AG.RE.F. (National Agricultural Research Foundation) in Thessaloniki and the Balkan Botanic Garden of Kroussia (ΒΒΚΚ), receiving scientific support and guidance from Dr. Eleni Maloupa, researcher and Head of ΒΒΚΚ. Rare and endemic plants collected in Cephalonia by a team under the supervision of Dr. N. Krigas, associate Plant Taxonomist of the Balkan Botanic Garden of Kroussia, are continuously being added to the garden of Cephalonia Botanica. The seeds of the plants are taxonomically certified and reproduced in the Laboratory of the National Agricultural Research Foundation for the Preservation and Evaluation of the Natural Cultivable Species in Thessaloniki. They are then returned to Cephalonia Botanica as plants with access number. In the context of this collaboration, Cephalonia Botanica is becoming a true Botanic Garden dedicated to the preservation of rare, endemic and endangered plants of the Ionian Islands. Cephalonia Botanica is a member of the National Network of Botanic Gardens of Greece, which includes gardens from Kroussia, Chios, Crete, Athens and Cephalonia. The Network will draw up a national action plan for the preservation of the Greek flora. In the context of this network, Cephalonia Botanica will cover the flora of the Ionian Islands, as well as the flora of Western Greece.

A specialized research programme completed in 2006 concerned the systematic identification of wild and endemic plants on the grounds of Cephalonia Botanica itself. In the context of this programme, Biologist Parthenopi Parcharidou collected plant samples, photographed and dried them in order to be taxonomically identified by the National Agricultural Research Foundation and the Aristotelian University of Thessaloniki. These samples form the initial material of the Herbarium of Cephalonia Botanica.