Native iron has been identified in an active thermogenic travertine deposit, located at Ilia area (Euboea Island, Greece). The deposit is forming around a hot spring, which is part of a large active metallogenetic hydrothermal system depositing ore-bearing travertines. The native iron occurs in two shapes: nodules with diameter 0.4 and 0.45 cm, and angular grains with length up to tens of µm. The travertine laminae around the spherical/ovoid nodules grow smoothly, and the angular grains are trapped inside the pores of the travertine. Their mineral-chemistry is ultra-pure, containing, other than Fe, only Mn (0.34–0.38 wt.%) and Ni (≤0.05 wt.%). After evaluating all the possible environments where native iron has been reported up until today and taking under consideration all the available data concerning the study area, we propose two possible scenarios: (i) Ilia's native iron has a magmatic/hydrothermal origin i.e., it is a deep product near the magmatic chamber or a peripheral cooling igneous body that was transferred during the early stages of the geothermal field evolution, from high temperature, reduced gas-rich fluids and deposited along with other metals in permeable structural zones, at shallow levels. Later on, it was remobilized and mechanically transferred and precipitated at the Ilia's thermogenic travertine by the active lower temperatures geothermal fluids; (ii) the native iron at Ilia is remobilized from deep seated ophiolitic rocks, originated initially from reduced fluids during serpentinization processes; however, its mechanical transport seems less probable. The native iron mineral chemistry, morphology and the presence of the other mineral phases in the same thermogenic travertine support both hypotheses.