A procedure for the immobilization of rhizomycelia of two strains of anaerobic fungi, namely Piromyces sp. KSX1 and Orpinomyces sp. 478P1 using Ca-alginate beads has been developed. Zoospores were found to be suitable propagules for the immobilization of the monocentric strain KSX1 giving rise to colonization in 100% of beads. For polycentric strain 478P1, which produced very few zoospores, partially homogenized rhizomycelia proved a suitable inoculum for the beads. The distribution of rhizomycelial growth inside the beads and on the surface depended on which fungal strain was immobilized. Strain 478P1 grew as a mycelial network inside the beads whereas strain KSX1 grew in microcolonies throughout the bead and on the surface, and was unable to evenly colonize the entire Ca-alginate matrix.