Recent findings have shown that humans can adapt their internal control model to account for the changing dynamics of systems they manipulate. In this paper, we explore the effects of magnitude and phase cues on human motor adaptation. In our experiments, participants excite virtual second-order systems at resonance via a two-degree of freedom haptic interface, with visual and visual plus haptic feedback conditions. Then, we change the virtual system parameters and observe the resulting motor adaptation in catch trials. Through four experimental conditions we demonstrate the effects of magnitude and phase cues on human motor adaptation. First, we show that humans adapt to a nominal virtual system resonant frequency. Second, humans shift to higher and lower natural frequencies during catch trials regardless of feedback modality and force cues. Third, participants can detect changes in natural frequency when gain, magnitude, and phase cues are manipulated independently. Fourth, participants are able to detect changes in natural frequency when the feedback (visual or visual plus haptic) is delayed such that the phase shift between the nominal system and catch trial system is zero. The persistent ability of participants to perform system identification of the dynamic systems which they control, regardless of the cue that is conveyed, demonstrates the human's versatility with regard to manual control situations. We intend to further investigate human motor adaptation and the time for adaptation in order to improve the efficacy of shared control methodologies for training and rehabilitation in haptic virtual environments.