The aim was to assess the phytochemical composition, phenolic component levels, and biological properties of the flowering tops of Origanum compactum and Origanum elongatum. The study employed phytochemical assays, spectrophotometric techniques for quantitative analysis of polyphenols, flavonoids, and tannins, and compound identification using HPLC/UV-ESI-MS. The antimicrobial, antioxidant, anticoagulant, and antidiabetic properties were examined both in vitro and in vivo. The results showed that the O. compactum extract had significantly high levels of total polyphenols, measuring 47.368 mg gallic acid equivalents per gram, and flavonoids, measuring 14.839 mg quercetin equivalents per gram. The phytochemical examination of O. compactum revealed that lithospermic acid accounted for 36.82 % of the chemicals detected, followed by salvianolic acid C at 12.57 % and ros-marinic acid at 6.01 %. The main constituents of O. elongatum are salvianolic acid C (14.46 %), luteolin-3-O-glucuronide (13.51 %), salvianolic acid B (12.24 %), rosmarinic acid (7.83 %), and rutin (6.18 %). The results demonstrated different levels of effectiveness against the investigated microorganisms, with the extract from O. compactum exhibiting better activity, particularly against Gram-negative bacteria, certain yeasts, and the fungus Aspergillus niger. The aqueous extracts of both Origanum species demonstrate significant antioxidant activity. O. compactum has a higher total antioxidant capacity (IC50 of 35.083 μg/mL) compared to O. elongatum (IC50 of 77.080 μg/mL). However, O. elongatum has a higher reducing power (35.697 μg/mL) compared to O. compactum (42.563 μg/mL). In vivo evaluations revealed that the aqueous extracts of O. compactum and O. elongatum possess significant antihyperglycemic and anticoagulant properties. The extracts demonstrated a marked reduction in blood glucose levels during the oral glucose tolerance test (OGTT) in Wistar rats and effectively prolonged both prothrombin time (PT) and activated partial thromboplastin time (aPTT), highlighting their ability to inhibit coagulation pathways. Moreover, their comparable efficacy to standard antihyperglycemic medications and absence of severe toxicity, even at high doses, underscore their therapeutic potential for safe and effective treatment applications. Between the two species, O. compactum exhibited superior efficacy in key biological activities such as antioxidant, antimicrobial, and anticoagulant properties, making it a strong candidate for therapeutic applications. This study underscores the value of Origanum species as a rich source of bioactive compounds, offering significant potential in pharmaceuticals, nutraceuticals, and agri-food industries. The findings pave the way for further exploration of their diverse applications.