This paper proposes a method for estimating traffic state from data collected by the advanced probe vehicles, namely, probe vehicles with spacing measurement equipment. The probe vehicle data are assumed to include spacing information, in addition to conventional position information. The spacing information is collected as secondary products from advanced vehicle technologies, such as automated vehicles. Traffic states and a fundamental diagram are derived from the probe vehicle data. Then, a traffic state estimator based on a data assimilation technique and a traffic flow model is formulated. This procedure is intended to mitigate negative effects in traffic state estimation caused by high fluctuations in microscopic vehicular traffic. The validation results with a simulation experiment suggested that the proposed method works reasonably, for example, the proposed method was able to estimate precise traffic state compared with the previous methods. Therefore, we expect that the proposed method can estimate precise traffic states in wide area where the advanced probe vehicles are penetrated, without depending on fixed sensor infrastructures nor careful parameter calibration.