A condition called “cypress mortality” affects forest of Austrocedrus chilensis (D. Don) Pic. Ser et Bizarri in Argentina. Their classic groups of symptoms has been described as a slow process of defoliation that culminating in death of the tree; nevertheless, dying and recently dead trees with abundant foliage are frequently observed in which foliage changes to red. Cinara (Cupressobium) cupressi (Buckton) is considered the agent responsible for reddening this indigenous conifer in Chile. Therefore, the relationship between the presence of C. cupressi and the new aerial symptoms in A. chilensis from Argentina required evaluation. However, Cinara (Cupressobium) tujafilina (del Guercio) also has been reported from this host, and the differentiation of both species of Cinara is time consuming and requires a great expertise because they share many morphologic and microscopic characters. A rapid molecular method of identification of C. cupressi and C. tujafilina is desirable to detect and differentiate them. We report the development and evaluation of a polymerase chain reaction-restriction fragment length polymorphism method based on the mitochrondial cytochrome oxidase I gene to identify C. cupressi and C. tujafilina in colonies of aphids. The first detection of C. cupressi from A. chilensis in Argentina, is reported based on the new method.