The need for automated methods to detect and extract marine mammal vocalizations from acoustic data has increased in the last few decades due to the increased availability of long-term recording systems. Automated dolphin whistle extraction represents a challenging problem due to the time-varying number of overlapping whistles present in, potentially, noisy recordings. Typical methods utilize image processing techniques or single target tracking, but often result in fragmentation of whistle contours and/or partial whistle detection. This study casts the problem into a more general statistical multi-target tracking framework, and uses the probability hypothesis density (PHD) filter as a practical approximation to the optimal Bayesian multi-target filter. In particular, a particle version, referred to as a Sequential Monte Carlo PHD (SMC-PHD) filter, is adapted for frequency tracking and specific models are developed for this application. Based on these models, two versions of the SMC-PHD filter are proposed and their performance is investigated on an extensive real-world dataset of dolphin acoustic recordings. The proposed filters are shown to be efficient tools for automated extraction of whistles, suitable for real-time implementation.