We present the first three-dimensional multi-species ionospheric model for Ganymede, based on a test particle Monte Carlo approach. Inputs include the electromagnetic field configuration around the moon from the magnetospheric models developed by Leclercq et al. (2016) and by Jia et al. (2009), and the number density, bulk velocity and temperature distributions of the neutral exosphere simulated by Leblanc et al. (2017). According to our simulations, O<sub>2</sub><sup>+</sup> is the most abundant ion species, followed by O<sup>+</sup>, H<sub>2</sub><sup>+</sup> and H<sub>2</sub>O<sup>+</sup>. For O<sup>+</sup> and O<sub>2</sub><sup>+</sup>, the majority of ions produced impact the moon's surface, while for the other species the majority escapes Ganymede's magnetosphere. For all ion species, the escape occurs either in the direction of corotation of the Jovian plasma or through the Alfvén wings.To validate our model, the output of our simulations, performed under the Galileo G2 flyby conditions, are compared to the observations. These include the electron density derived by the plasma wave instrument (PWS), the ion energy spectrogram measured by the plasma analyzer (PLS) and the associated plasma moments (Frank et al., 1997a).On the one hand, the electron density found by our model is consistently underestimated throughout the flyby, being at least one order of magnitude lower compared to observations. We argue that the prime reason for this discrepancy comes from the exospheric density, which may be underestimated. On the other hand, we find a remarkably good agreement between the modeled ion energy spectrogram and that recorded by PLS, providing a validation of the test particle model. Finally, we compare the modeled plasma moments along the G2 flyby with those analyzed by Frank et al. (1997a). The data seems to be more consistent with an ionosphere dominated by O<sub>2</sub><sup>+</sup> instead of H<sup>+</sup> or O<sup>+</sup>, as suggested previously in the literature. This supports our finding that O<sub>2</sub><sup>+</sup> is the dominant ion species close to the surface.