In the field of civil infrastructure, Structural Health Monitoring systems are implemented more and more frequently with the aim to safeguard the safety and service-life of structures such as bridges and tunnels. Changes in the integrity of the material and/or structural properties of this class of structures is known to adversely affect their performance, which can also be observed from the structures’ dynamic response, such as the natural frequencies, damping ratios and mode shapes. The procedure to obtain these response parameters is known as modal analysis. Two methods for obtaining these parameters are compared in this paper, one based on a careful analysis of measured vibration sensor data, and another one is based on a structural calculation using a Finite Element Method (FEM). The dynamic modal characteristics of a structure can be obtained by using vibration-based damage identification techniques such as Stochastic Subspace Identification (SSI). The SSI technique is capable of extracting modal parameters from output-only measurements, i.e. using raw data collected by simply monitoring a structure under its normal load. In this paper the application of SSI for the “Hollandse Brug”, which is a six-lane Dutch concrete highway bridge under in-service conditions, is described. The bridge is equipped with a sensor network of 145 sensors, including 34 vibration sensors (geo-phones). This paper demonstrates how the key modal parameters can be extracted by applying SSI to the sensor readings. To assess the quality of the sensor-based results, the modal parameters derived using SSI are compared with the results obtained from Finite Element Method (FEM) calculations. For the FEM calculation, the computer program Scia Engineer is used. The results of the two methods agree well, which shows that the SSI technique under output-only and in-service conditions is an effective tool for modal analysis, and thus a valuable method to be used in structural health monitoring systems.