The enigmatic snake genus Micrelaps has uncertain phylogenetic affinities. The type species of the genus, Micrelaps muelleri, inhabits the Southern Levant. Snakes inhabiting the Jordan River Valley just south of the Sea of Galilee have been described as a new species, Micrelaps tchernovi, based on their distinct colour patterns, despite M. muelleri being well known to be variable in colour-pattern traits. Here we use morphological and molecular data to examine the taxonomic status and phylogenetic affinity of Levantine Micrelaps. We show that all scalation, colour, and pattern-related traits are extremely variable across the range of these snakes. Some morphological features show clinal variation related to temperature and precipitation, and snakes with a ‘tchernovi’ morph are merely at one end of a continuum of morphological variation. Both ‘classical muelleri’ and ‘tchernovi’ morphs occur in syntopy in the Jordan Valley and elsewhere in Israel. Against this background of high morphological variation, neutral genetic markers show almost no differentiation between snakes, no genetic structure is evident across populations, and no differences are to be found between the two putative species. We conclude that Levantine Micrelaps belongs to a single, morphologically variable, and genetically uniform species, Micrelaps muelleri, of which M. tchernovi is a junior synonym.