An expansion of the use of molecular data in the 21st C has accompanied a greatly increased number of amphibian and reptile species descriptions. Some of the newly discovered or recognised diversity has been considered ‘cryptic’. Islands and island endemic taxa represent worthwhile systems to address questions about cryptic species. Being comprised of multiple islands of partly Gondwanan origin, the Seychelles Archipelago offers the opportunity to address crypsis for a biota comprised of both deep-time vicariant and more recent overwater dispersed forms. We focus on the history of discovery, taxonomy, inter- and intraspecific variation, and phylogeography. Most recent studies investigating intraspecific variation in Seychelles herpetofauna have identified (often similarly) geographically structured, genetically divergent populations, and we note the potential of Seychelles herpetofauna in understanding lineage crypsis. We attempt to assess why some lineages have remained cryptic for so long; whether recently discovered lineages are truly cryptic and/or distinct taxa; and if ecology (vagility) and/or length of time on the islands can explain lineage crypsis. Patchy data and/or lack of sufficient study currently limit possible interpretations. Detailed ecological and environmental data, population genetic assessments, reconstruction of phylogeographic histories, and integration of phenotypic trait data will all aid future assessments.