The effects of diatom frustule shape and heat treatment process on the compressive mechanical properties of an epoxy matrix were experimentally investigated. Different pennate diatoms reduced to exclusive species by isolating and culturing were used as filler in the epoxy matrix. A commercial diatomite was heat treated between 600oC and 1200oC to increase the crystallinity. Filling epoxy matrix with ~6 wt% of natural commercial diatomite and Achnanthes taeniata frustule increased the compressive strength from 60 MPa to 67 MPa and 79 MPa, respectively. A higher strengthening, ~10 MPa, and moduli with Achnanthes taeniata frustule addition was found. The heat treatment of natural diatomite frustules at 1000oC increased both compressive strength and stress values of the epoxy matrices. The compressive strength increased from 60 to 90 MPa with the heat-treatment process, providing 50% of increase in the compressive strength of neat epoxy.