Numerous species from the classes Amphibia and Reptilia are facing extinction as a result of habitat loss and increasing anthropogenic impact on the environment; to be more specific, 32% amphibian and 20% reptilian species are either threatened or endangered. The aim of this review is to highlight the status of biobanking as one of the many tools within conservation of amphibians and reptilians. Moreover, we discuss opportunities and challenges as well as provide recommendations for future conservation and management strategies for saving vulnerable species from the two taxa. Previous studies have reported production of viable offspring from cryopreserved amphibian germplasm and in reptiles from cooled spermatozoa. However, further research is needed to improve the efficiency of cryopreserved germplasms for future use in biobanks. More advanced research directions include culture of fibroblast cell lines coupled with appropriate pluripotent stem cells and advanced reproductive technologies as this will represent one further unique and invaluable resource in species conservation and management.