Recent experiments in the underdoped regime of the hole-doped cuprates have found evidence for an incommensurate charge density-wave state. We present an analysis of the charge ordering instabilities in a metal with antiferromagnetic correlations, where the electronic excitations are coupled to the fractionalized excitations of a quantum fluctuating antiferromagnet on the square lattice. The resulting charge density-wave state emerging out of such a fractionalized Fermi liquid (FL∗) has wave vectors of the form (±Q0,0),(0,±Q0), with a predominantly d-form factor, in agreement with experiments on a number of different families of the cuprates. In contrast, as previously shown, the charge density-wave instability of a nearly antiferromagnetic metal with a large Fermi surface, interacting via short-range interactions, has wave vectors of the type (±Q0,±Q0). Our results show that the observed charge density-wave appears as a low-energy instability of a fractionalized metallic state linked to the proximity to an antiferromagnetic insulator, and the pseudogap regime can be described by such a metal at least over intermediate length and energy scales. © 2014 American Physical Society.