The disclosure relates to a cotton variety, designated PX499090W3FE, the plants and seeds of the cotton variety PX499090W3FE, methods for producing a cotton plant, either varietal or hybrid, produced by crossing the cotton variety PX499090W3FE, with itself or with another cotton plant, hybrid cotton seeds and plants produced by crossing the variety PX499090W3FE with another cotton variety or plan, 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 PX499090W3FE, to methods for producing other cotton varieties derived from cotton variety PX499090W3FE, and to the varieties derived by the use of those methods.