The RTe3 (R = rare earth) family of layered van der Waals (vdW) compounds hosts coexisting magnetic and charge density wave (CDW) orders, yet the interplay between these degrees of freedom remains largely unexplored. Combining polarized and unpolarized neutron diffraction on single crystals of HoTe3, we identify two distinct antiferromagnetic (AFM) phases, both exhibiting a collinear ↑↑↓↓ motif within individual vdW layers. The two phases are distinguished by the vdW stacking of magnetic layers: ferromagnetic (FM) stacking in the higher-temperature AFM-II phase, here termed “vertical-stripe”, and AFM stacking in the AFM-I ground state, here termed “tilted-stripe”; the two phases have propagation vectors qm2 = (0.48, 0, 0) and qm1 = (0.5, 0.5, 0), respectively. In contrast to the CDW-driven exotic magnetism in DyTe3, TbTe3, and GdTe3, we find no evidence for coupling between magnetism and CDW in HoTe3. The presence of a checkerboard-type charge order in HoTe3 may be detrimental for realizing coupled spin/charge order parameters in layered vdW systems.