Multiple magnetic skyrmion phases add an additional degree of freedom for skyrmion based ultrahigh-density spin memory devices. Extending the field to two-dimensional van der Waals magnets is a rewarding challenge, where the realizable degree of freedoms (e.g. thickness, twisting angle and electrical gating) and high skyrmion density result in intriguing new properties and enhanced functionality. We report a van der Waals interface, formed by two 2D ferromagnets Cr2Ge2Te6 and Fe3GeTe2 with a Curie temperature of ~65 K and ~205 K, respectively, hosting two groups of magnetic skyrmions. Two sets of topological Hall effect are observed below 60 K when Cr2Ge2Te6 is magnetically ordered. These two groups of skyrmions are directly imaged using magnetic force microscopy. Interestingly, the magnetic skyrmions persist in the heterostructure in the remanent state with zero applied magnetic field. Our results are promising for the realization of skyrmionic devices based on van der Waals heterostructures hosting multiple skyrmion phases.