Thalénite-(Y), ideally Y3Si3O10F, is a heavy-rare-earth-rich silicate phase occurring in granite pegmatites that may help to illustrate rare-earth element (REE) chemistry and behaviour in natural systems. The crystal structure and mineral chemistry of thalénite-(Y) were analysed by electron microprobe analysis, X-ray diffraction and micro-Raman spectroscopy from a new locality in the peralkaline granite of the Golden Horn batholith, Okanogan County, Washington State, USA, in comparison with new analyses from the White Cloud pegmatite in the Pikes Peak batholith, Colorado, USA. The Golden Horn thalénite-(Y) occurs as late-stage sub-millimetre euhedral bladed transparent crystals in small miarolitic cavities in an arfvedsonite-bearing biotite granite. It exhibits growth zoning with distinct heavy-rare-earth element (HREE) vs. light-rare-earth element (LREE) enriched zones. The White Cloud thalénite-(Y) occurs in two distinct anhedral and botryoidal crystal habits of mostly homogenous composition. In addition, minor secondary thalénite-(Y) is recognized by its distinct Yb-rich composition (up to 0.8 atoms per formula unit (apfu) Yb). Single-crystal X-ray diffraction analysis and structure refinement reveals Y-site ordering with preferential HREE occupation of Y2 vs. Y1 and Y3 REE sites. Chondrite normalization shows continuous enrichment of HREE in White Cloud thalénite-(Y), in contrast to Golden Horn thalénite-(Y) with a slight depletion of the heaviest REE (Tm, Yb and Lu). The results suggest a hydrothermal origin of the Golden Horn miarolitic thalénite-(Y), compared to a combination of both primary magmatic followed by hydrothermal processes responsible for the multiple generations over a range of spatial scales in White Cloud thalénite-(Y).