Filago wagenitziana, discovered in 2008 in western Kriti (Crete), is described as a new species, illustrated and compared with similar species of the genus. This dwarf annual is a local endemic of the easternmost spurs of the Lefka Ori (White Mountains), growing between 700 and 800 m in altitude. It is restricted to open, shallow, semi-wet quartzite soil, chiefly in semi-shady conditions in or next to mixed mesophilous woodland with Platanus orientalis. The total known population of F. wagenitziana consists of very few subpopulations, comprising perhaps less than 1000 plants, in an area of about 1 km². This small area, which also harbours the only Sphagnum spring fen in Crete, lies only just outside the Natura 2000 site Asfendou-Kallikratis. The habitat of F. wagenitziana and its surroundings are endangered by water exploitation.