In many complex genetic syndromes, various distinct capillary nevi may serve as diagnostic clues. To render dermatologists in practice capable of recognizing and classifying such cutaneous markers. On the basis of the literature and own observations, this review describes 14 different syndromes associated with capillary nevi that can be recognized by dermatologists as a diagnostic indication. The following capillary nevi can be distinguished for syndrome recognition: nevus flammeus of the Sturge-Weber syndrome (GNAQ), port-wine nevus of the Proteus type (AKT1), port-wine nevus of the PIK3CA-related overgrowth spectrum (PROS) type, midfacial port-wine patch of the PROS type, reticulate capillary nevus heralding megalencephaly-capillary nevus syndrome that is likewise part of PROS, cutis marmorata telangiectatica congenita (van Lohuizen syndrome), nevus roseus, nevus vascularis mixtus, rhodoid nevus (RASA1), nevus anemicus as a diagnostic indication of neurofibromatosis 1 and Carter-Mirzaa macules (STAMBP). A diagnostic difficulty lies in the fact that not all syndromes associated with capillary nevi have been elucidated at the molecular level. For this reason, the preliminary dimension of the present review should be borne in mind. On the other hand, dermatologists in practice now have the fascinating chance to stimulate further advances in this particular field of knowledge by asking experts in dermatology, pediatrics or medical genetics how to solve the problem of molecular syndrome recognition in a puzzling case.