The essential oils obtained from the aerial parts of Origanum scabrum and Origaum microphyllum, both endemic species in Greece, were analyzed by means of GC and GC-MS. Forty-eight constituents were identified, representing 98.59 and 98.66% of the oils, respectively. Carvacrol, terpinen-4-ol, linalool, sabinene, alpha-terpinene, and gamma-terpinene were found as the major components. Furthermore, both samples exhibited a very interesting antimicrobial profile after they were tested against six Gram-negative and -positive bacteria and three pathogenic fungi.