The natural durability of wood to mold fungi was tested under laboratory conditions with locally sourced Citharexylum spinosum and Morus alba woods. The mold fungi were Penicillium selerotigenum, Paecilomyces variotii, and Aspergillus niger. Changes in surface elemental composition were evaluated with energy dispersive X-ray spectroscopy (EDX) and the biodeterioration of wood surfaces by scanning electron microscope (SEM). The C peak element of C. spinosum wood was affected significantly (P = 0.0004) and decreased from 49.91% in the control specimens to 47%, 40.1%, and 40% with P. selerotigenum, A. niger, and P. variotii, respectively. Also, the C peak element of M. alba heartwood significantly decreased (P < 0.0001) from 51.33% in the control specimens to 41.49%, 45.66%, and 43.66% in wood inoculated with A. niger, P. variotii, and P. selerotigenum, respectively. The elements Al and Cu were observed in high percentages with M. alba heartwood inoculated by P. variotii. The methanol extract from M. alba heartwood showed good inhibition against the growth of A. niger at a concentration of 32 μg/mL, and the methanol extract from C. spinosum wood showed remarkable inhibition against the growth of P. variotii at a concentration of 8 μg/mL. The results of this study clearly showed the changes that occur in wood samples as a result of fungal infestation.