Despite the great importance of the siphons for infaunal bivalves, only a few studies have examined their tissues using histology techniques or scanning electron microscopy. In the present study, the siphons of Tellina lineata Turton, 1819 and Macoma biota Arruda & Domaneschi, 2005 were investigated. The siphon walls are composed by a series of muscle sheets of longitudinal ("L"), circular ("C") and radial ("R") fibers, with a clear pattern common to both species: there is a main median longitudinal layer (Lm), and two peripheral circular layers, one inner (Ci) and one outer (Co), near the epithelia. A median circular layer (Cm) separates an internal (Lmi) from an outer (Lmo) median longitudinal layer. Further, the Co is split by a thin outer longitudinal layer (Lo), forming Coi and Coo layers, the former being obliquely oriented. Thin radial fibers (R) delimit clear packages of Lmi and Lmo fibers. In each siphon, there are six longitudinal nerve cords, running within the Lmi layer, adjacent to the Cm. The inhalant and exhalant siphons of M. biota are very similar in structure, but the Lmo of the exhalant siphon is almost twice as thick as its Lmi, while in the inhalant siphon these layers have similar thicknesses; the Coi is very thick, especially in the exhalant siphon. The inhalant siphon of T. lineata is very similar to that of M. biota, differing only with respect to the thickness of the Coi, which in the former species is not as well developed as in the latter. The Lmo of the exhalant siphon of T. lineata is by far the most developed layer, with the Lmi represented only by uniseriate small cells; in the vicinities of the nerve cords, the Cm is split in two layers. The epithelia of both siphons of M. biota and T. lineata bear ciliated receptors, which were difficult to observe as they were frequently covered with mucus. It was possible to observe that cilia are present in both species, differing in length and in the number per receptor between the inhalant and exhalant siphons, and between the species. Detailed comparisons among the siphons of M. biota and T. lineata and other bivalve species are very difficult, because of at least two reasons. First, each investigator has used different methods to prepare and observe the siphons through histological sections; and second, different nomenclatural schemes are used to describe the musculature of the siphons, causing confusion when the same layers are compared among different species. In order to unify the nomenclature of tissue layers of the bivalve siphons, we now propose a scheme to name these layers based on topological homology.