In recent years, molecular species delimitation has become a routine approach for quantifying and classifying biodiversity. Barcoding methods are of particular importance in large-scale surveys as they promote fast species discovery and biodiversity estimates. Among those, distance-based methods are the most common choice as they scale well with large datasets, however, they are sensitive to similarity threshold parameters and they ignore evolutionary relationships. The recently introduced Poisson Tree Processes (PTP) method is a phylogeny-aware approach that does not rely on such thresholds. Yet, two weaknesses of PTP impact its accuracy and practicality when applied to large datasets, it does not account for divergent intraspecific variation and is slow for a large number of sequences.