Polyhydroxylalkanoates (PHA) produced by the fermentation of bacteria or other microorganisms are also fully biodegradable polyesters with a wide array of properties that range from stiff thermoplastics to elastomers. Nevertheless, the processability and the brittleness of some PHA remains the major problem in applications. Many methods have been developed to increase the properties of biopolymers, such as random and block copolymerization, chemical modification or incorporation of numerous fillers, which modulate both the biodegradation rate and the mechanical properties of the final products. Biocomposites have attracted more attention in the last decades, since physical blending is another effective and simple way to prepare biodegradable polymers reinforced by natural fillers with different morphologies and physical characteristics. In this work, different kinds of blends of polyhydroxylalkanoates, i.e. poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) and poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (PHBHHx), and containing various fillers (Cloisite, sepiolite and Aloe Vera) were prepared by melt compounding, with and without previous polymer compatibilization. The effects of the filler incorporation on the polymer morphology and composite properties were also investigated. The influence of the filler chemical treatment is discussed as well as the effect of the polymer compatibilization. A synergistic effect of compatibilizer and filler was highlighted leading to an improved miscibility of the systems.