The disclosure relates to a cotton variety, designated PHY499WRF, the plants and seeds of the cotton variety PHY499WRF, methods for producing a cotton plant, either varietal or hybrid, produced by crossing the cotton variety PHY499WRF with itself or with another cotton plant, hybrid cotton seeds and plants produced by crossing the variety PHY499WRF with another cotton variety or plant, methods for producing a cotton plant containing in its genetic material one or more transgenes, and the transgenic cotton plants produced by that method. This disclosure also relates to cotton varieties derived from cotton variety PHY499WRF, to methods for producing other cotton varieties derived from cotton variety PHY499WRF, and to the varieties derived by the use of those methods.