The main difference between the sponge genera Leucilla and Paraleucilla (Porifera, Calcarea, Amphoriscidae) is the presence of a disorganized zone (DZ) in the inner region of the skeleton of the latter genus. However, it has been repeatedly observed that specimens from different species of Paraleucilla lack this feature. It is assumed that the size of the sponge may have an effect on the presence or the absence of the DZ, but no investigation of this morphological variation has previously tested this hypothesis. Here, we examined this assumption and described the frequency with which the DZ is absent from individuals of Paraleucilla magna. We also investigated possible drivers of the observed variation using generalized linear models to evaluate whether the month of the year, rainfall, reproductive activity, volume, and body wall thickness could influence the presence or the absence of the DZ. The DZ was absent from 46.5% of the analyzed individuals, indicating that it may be misleading to use this trait to identify the genera Leucilla and Paraleucilla. The presence of the DZ in P. magna is influenced negatively by volume and positively by body wall thickness of the individuals. Our results confirm the previous assumptions for the family Amphoriscidae and highlight problems with the current classification of Calcarea. A discussion of the validity of some morphological characters and the importance of analyzing their variation is provided.