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Flanagan produces small amounts of Cabernet Sauvignon, Chardonnay, Syrah and tiny amounts of Pinot Noir. A site was acquired in Bennett Valley in 1999 and planted to Cabernet Sauvignon, Merlot and Syrah. The winemaker is French-born Phillipe Melka (Dominus and consultant).
In 2011, Eric Flanagan bought a 56-acre ranch in Windsor from Joe Martin, the founder of St. Francis Winery & Vineyards. The ranch included 29 acres planted to Chardonnay and Pinot Noir. Chardonnay clones are primarily Wente and Robert Young, and Pinot Noir clones are Swan and Pommard.
Flanagan also owns the Platt Vineyard, west of Sebastopol. Former proprietors Lou and Joan Platt sold grapes to Littorai, Ramey and Red Car, and they still sell fruit to others, but cherry-pick for Flanagan Wines.
Flanagan wines are sold through the winery's online store.