Carrageenan (CRG) and carrageenan/chitosan (CH) gel beads (CRG/CH) were prepared as a release delivery system for echinochrome A (Ech). According to spectral data, the Ech was dispersed in the polymer matrix, interacted with CRG, was not oxidised, and remained stable after encapsulation in CRG beads. Carrageenan beads containing Ech were coated with CH by layering. The influence of the structural features of CRG on the formation of beads and the beads morphology, swelling behaviour, mucoadhesive properties and drug release were evaluated. The polysaccharide matrices with Ech showed different swelling characteristics depending on the pH of the medium and the structure of the CRG used. The slow drug release from polysaccharide matrixes was observed for κ- and κ/β-CRG beads, that contained 3,6-anhydro-α-d-galactopyranose units and had high molecular weight. The obtained results showed the prospects of using polysaccharide beads to include Ech.