A colonial lifestyle necessitates communication between colony members to coordinate functions and enable resource sharing through physiological integration. Colonial integration is predicted to increase with both the size of the colony and the level of specialization (polymorphism). In modular colonies, although integration might be reflected in structural characteristics such as module spacing or branching patterns, physiological integration is fundamentally dependent on the level of connectedness between modules. In cheilostome bryozoans, funicular tissue links adjacent zooids through pores within zooid walls and is the most likely means of nutrient transport within colonies. We sought to determine whether the relative numbers of pores (septulae) and pore plates (septal chambers) per zooid differed across colony regions in a monomorphic species, Watersipora subtorquata, and one showing some polymorphism, Mucropetraliella ellerii. Within each species, the morphology of pore plates corresponded to functional predictions based on their position within the zooid, and connection numbers per zooid increased with colony size. Contrary to expectations, however, the more complex species, M. ellerii, had significantly fewer porous connections per zooid than W. subtorquata. Physiological connectedness was therefore not predicted by simple assessment of polymorphism in these species and may not be sufficient to infer colonial integration in related taxa.