The study of multiplicative noise models has a long history in control theory but is re-emerging in the context of complex networked systems and systems with learning-based control. We consider linear system identification with multiplicative noise from multiple state-input trajectory data. We propose exploratory input signals along with a least-squares algorithm to simultaneously estimate nominal system parameters and multiplicative noise covariance matrices. Identifiability of the covariance structure and asymptotic consistency of the least-squares estimator are demonstrated by analyzing first and second moment dynamics of the system. The results are illustrated by numerical simulations.