Carbonate biomineralization normally occurs in three distinct types: controlled, induced and influenced, each with its peculiar characteristics. Building-reef species within the family Cirratulidae (Annelida, Polychaeta) constitute the first known example of “double-phased” biomineralization among marine invertebrates, as they combine controlled and influenced biomineralization types in the process of developing carbonate tube aggregates. The ultrastructure of the tubes, composed of thin calcareous lamellae with a spherulitic prismatic ultrastructure, as well as lamellae with a homogeneous structure, is produced directly by the worms living inside them and clearly indicates a controlled biomineralization, while the calcareous matrix with agglutinated xenolithic granules that fills the areas between the tubes of the same aggregate is the product of an influenced biomineralization.The reason why this biomineralization process occurs is yet unknown. This study is therefore aimed at describing in detail for the first time the biomineralization of Miocene (Diplochaetetes) and Recent (Dodecaceria) tubes of cirratulid aggregates from southern Peru via optical microscopy, epifluorescence, SEM and EDS analyses. Furthermore, a detailed morphometric and compositional study of tubes was performed and results were statistically evaluated. The comparison with recent cirratulids allowed the recognition of the double-phased biomineralized skeletons in the fossil specimens, despite the different degree of recrystallization which affected the studied Peruvian bioconstructions. This observation suggests that this type of biomineralization has not changed over the course of the entire Cenozoic and can be considered a unique evolutionary character which probably was developed by these polychaetes to be safer from predators, as well as generally more stable and more resistant to environmental stressing factors.