Low-temperature omphacite has peculiar microstructures called ‘antiphase domains (APDs)’, which can be formed via phase transition from disordered C2/c to ordered P2/n structure during cooling. Hence morphological analyses of the APDs of undeformed omphacite have a potential to unravel the temperature–time (T–t) histories of the eclogite. We investigated five omphacite inclusions in a euhedral garnet porphyroblast obtained from low-temperature eclogite in Syros. The garnet (~6 mm in size) exhibits a distinct prograde chemical zoning and contains abundant mineral inclusions. Transmission electron microscope (TEM) observations of the focused ion beam (FIB) foils confirmed a heterogeneous distribution of equiaxed APDs (10–280 nm in diameter) and columnar APDs. Size distributions of the equiaxed APDs are characterized by kurtosis values of −0.45–3.91, which are larger than those in the matrix omphacite. The columnar APDs are subdivided into two types: dislocation-related (Type I) and inclusion–host interfacial (Type II). The presence of Type I APDs suggests the inclusions were deformed prior to the host garnet growth. In contrast, Type II APDs, which are characterized by a bundle of stripe-like APDs (~40 nm in width) aligned perpendicular to the host garnet, imply the simultaneous growth of omphacite and garnet in a non-deformation state. The presence of these two contrasting APDs of omphacite inclusions in the single prograde-zoned garnet prevents a simple application of geospeedometry based on APD sizes. Nevertheless, our observations demonstrate that APDs are keys to understanding thermodynamic equilibrium states and the mineral growth kinetics during eclogitization.