AbstractSymbiodiniaceae are crucial dinoflagellate symbionts for corals. They are affected by climate change‐induced temperature rises that lead to coral bleaching, impacting coral reefs' health. Cryopreservation offers a solution to ensuring long‐term storage of this species, preserving genetic diversity and viability. However, cryoinjury's impacts on glycan, a class of biomolecules with diverse biological roles including the initiation of coral–Symbiodiniaceae symbiosis, remain unknown. Thus, we examined the glycan profile of Breviolum psygmophilum cells cultured for varied periods post‐thaw. The cells were subjected to two‐step freezing with 2 M methanol as the cryoprotectant, and were cryopreserved for 2 h, then thawed and cultured. Lectin Array 70 was used to analyze glycan profiles of B. psygmophilum before and after cryopreservation. The results indicated that fucose and mannose differed significantly from N‐acetyllactosamine, indicating its low presence in non‐cryopreserved cells. Cryopreserved B. psygmophilum showed significant changes in fucose and mannose content, and several lectins contributed to the abundance of their respective carbohydrate moieties. These carbohydrates may affect cell division, repair, and energy. Lectins Gal1, CNL, DSA, BC2LCN, GRFT, HHA, NPA, Orysata, ConA, Gal3, and ACG changed in content post‐cryopreservation, which may have been to mitigate the cryopreservation‐induced stress, similar to their response to other stresses, while vital biological processes were maintained. This study sheds light on Symbiodiniaceae glycan profile alterations post‐cryopreservation, which could influence Symbiodiniaceae's ability to establish symbiosis with corals thus highlighting the need to optimize cryopreservation protocols to minimize glycan alterations and enhance Symbiodiniaceae preservation, ultimately supporting coral reef conservation efforts.