Ceresiosaurus is a secondarily marine reptile that lived during the Middle Triassic (Ladinian–Anisian) in a subtropical lagoonal environment with varying open marine influences. The genus comprises two species, Ceresiosaurus calcagnii and C. lanzi, and represents one of the largest vertebrate of up to 3-m snout-tail length from the UNESCO World Heritage site Monte San Giorgio, which is settled along the Swiss–Italian border. Earlier morphological studies identified this genus as basal sauropterygian still possessing many similarities with the plesiomorphic ancestral terrestrial condition. Interspecific morphological variation was interpreted as indicator for different habit(at) preferences by ascribing two locomotion types for each of the species. In this study, detailed data on the microstructure of the long bones are given and findings were put into a palaeoecological and phylogenetic context in comparison to other sauropterygians from Monte San Giorgio. Results showed that both Ceresiosaurus species retain a calcified cartilaginous core in the medullary region in at least young individuals. They both exhibit cyclical bone growth of lamellar to parallel-fibred bone matrices with undulating incremental growth marks and low to moderate vascularisation (lamellar-zonal bone tissue type). Interspecific variation comprises differences in the distribution of differently organised bone matrices and the size, orientation and number of vascularisation. The vascularisation pattern (abundance and orientation of the canals) of the pachyosteosclerotic long bones of C. calcagnii mostly resembles the histotype of the stratigraphically youngest pachypleurosaurid from Monte San Giorgio, Neusticosaurus edwardsii (except for the presence of primary osteons in the cortex of the former). The bone sample of C. lanzi is only osteosclerotic and most similar to young Nothosaurus (except for the irregular presence of fibrolamellar bone in the latter). The slightly different growth pattern already at young ontogenetic stages might be linked to a different mode of life within the restricted lagoonal basin for Ceresiosaurus, which supports previous studies on the morphological data that ascribed two different locomotion types.