To show the importance of plant-microbe association in stressed tropical landscapes, the study evaluated the physicochemical characteristics and indigenous arbuscular mycorrhizal fungi (AMF) spore density in selected vegetation patches of marginal upland soils in Central Philippines. Five quadrats were used in the study, namely Andropogon aciculatus (control plot), Imperata cylindrica, Chromolaena odorata, Melastoma malabathricum and mixed vegetation patch. Results showed that soils in the studied vegetation patches had different physicochemical characteristics and AMF spore density. Although all patches had clay soil texture and comparable water-holding capacity, mixed vegetation patch had moderate compaction (1.33 g cm-3) and higher porosity (50.31%) compared with the other patches, which had extreme compaction (1.37-1.65 g cm-3) and lower porosity (37.74-48.76%). In terms of chemical properties, soils in different patches had moderate (5.69) to strongly acidic pH (5.13), moderate organic matter (2.69-2.91%) levels, low P (2.67-3.94 ppm) content and above critical K levels (0.2-1.2 cmol+ kg-1). Results also revealed that C. odorata patch had the highest spore density count (11.33 spores 100 g-1), followed by mixed vegetation (9 spores 100 g-1), M. malabathricum (8.33 spores 100 g-1), and A. aciculatus patch having the lowest spore density count (4 spores 100 g-1). The significant spore density variability was attributed to the differences in soil’s physicochemical characteristics among the different vegetation patches and AMF host specificity. Spores detection, therefore, indicated AMF presence and helped the adaptation mechanism of the natural vegetation in this degraded upland.