The popularity of electronic identification keys for species identification has increased with the rapid technological advancements of the 21st century. Although electronic identification keys have several advantages over conventional textual identification keys and work well for charismatic species with large and clear morphological characters, they appear to be less feasible and less effective for species with cryptic morphology (i.e. small, obscure, variable characters and/or complicated structures associated with terminology that is difficult to interpret). This is largely due to the difficulty in presenting and illustrating cryptic morphological characters unambiguously. When taking into account that enigmatic species with cryptic morphology are often taxonomically problematic and therefore likely exacerbate the taxonomic impediment, it is clear that species groups with cryptic morphology (and all the disciplines dependent on their correct identification) could greatly benefit from a user-friendly identification tool, which clearly illustrates cryptic characters. To this end, the aim of this study was to investigate and develop best practices for the unambiguous presentation of cryptic morphological characters using a pilot interactive photographic identification key for the taxonomically difficult plant genus Thesium (Santalaceae), as well as to determine its feasibility. The project consisted of three stages: (1) software platform selection, (2) key construction and (3) key evaluation. The proposed identification key was produced with Xper3 software and can be accessed at http://www.xper3.fr/xper3GeneratedFiles/publish/identification/1330098581747548637/mkey.html. Methodologies relating to amongst others, character selection and delineation, visual and textual descriptions, key construction, character coding and key evaluation are discussed in detail. Seventeen best practices identified during this study are subsequently suggested for future electronic key compilation of species with cryptic morphology. This study indicates that electronic identification keys can be feasible and effective aids for the identification of species with cryptic morphological characters when the suggested best practices are followed.