The epidermal organs of an undescribed Phascolion species from the Balearic Islands were investigated using SEM, TEM, LM, CLSM and μCT methods. We found axial receptor cells confirming the previously assumed sensory function of epidermal organs. Our analyses also revealed six types of secretory cells. Some secretory cells types are capable of secreting filamentous and amorphous secretion in two different ways simultaneously (bimodal secretion). The high diversity of cell types, the complex pattern of acinar units, and the absence of a common gland pore make epidermal organs of Phascolion unique amongst sipunculans (Phascolion type). Our reconstruction of the evolution of the epidermal organs of Sipuncula revealed that Phascolion‐type epidermal organs may have derived from either Golfingia‐, Sipunculus‐ or Phascolosoma‐type epidermal organs. The oldest known sipunculans were Golfingia‐like and had epidermal organs, which might resemble the architecture of the Golfingia‐type epidermal organs in extant taxa. Thus, it can be hypothesized that bimodal secretory cells (e.g. basophilic secretory cells) were part of the sipunculan ground pattern. Moreover, bimodal secretory cells of Phascolion look strikingly similar to those found in various annelid glands and thus might even be part of the ground pattern of stem species of Sipuncula + Pleistoannelida.