Abstract
Nereididae comprises a diverse group of marine worms and is one of the most studied families in Annelida. However, phylogenetic relationships within the group are still poorly understood. Previous studies, based on morphological data, have disagreed on the membership of recognized subfamilies and, current taxonomy lacks sufficient phylogenetic underpinning. This study uses complete mitochondrial genome and transcriptome data to evaluate relationships within Nereididae and test currently employed subfamilies. Ancestral state reconstructions were performed to evaluate if morphological traits found in the pharynx, that is papillae and paragnaths, correspond with phylogenetic relationships based on mitochondrial data. Our results suggest that Nereidinae and Gymnonereidinae, as currently recognized, are not monophyletic groups. In general, molecular results suggest that morphological features used in nereidid taxonomy need re‐evaluation as they may be more evolutionary plastic than recognized. Ancestral state reconstruction suggests that papillae and paragnaths may have evolved early in the family and their presence, as currently employed in taxonomy, does not allow accurate diagnose of groups within Nereididae. In contrast, unique mitochondrial gene order defines at least one higher‐level clade within Nereididae.