We estimated the population density of the globally threatened Elfin-woods Warbler Setophaga angelae within two forest types at different elevations in the Luquillo Experimental Forest in north-eastern Puerto Rico. Population densities ranged from 0.01 to 0.02 individuals/ha in elfin woodland and 0.06–0.26 individuals/ha in palo colorado forest in 2006, with average rates of decline since 1989 of 0.002–0.01 and 0.003–0.06 individuals/ha respectively. These estimates show a significant general declining trend from c.0.2 individuals/ha in 1989 in elfin woodland to c.0.02/ha in 2006, and from 1 to 0.2 in palo colorado forest. Although variation in estimated population density depended on the statistical method used, we document and discuss possible causes of an overall population decline from 1989 to 2006, lending support to previous initiatives to reclassify the species from the IUCN Red List category of “Vulnerable” to “Endangered”.