Pines evolve with fire and have diverged into fire-avoiders and fire-adapters. Pine needles are resistant to microbial decomposition, and their accumulation serves as a major fuel source for forest fires. Facilitated needle decomposition reduces forest fuel loads and probably interacts with the adaptive strategies of pines. However, there is little information available regarding differences in microbiomes associated with needle decomposition of the two types of pine. In this study, we monitored the microbial communities in three compartments associated with needle decomposition, namely, fresh needles, needle litter, and humus, along altitudinal gradients at three sites of the fire-tolerator Pinus taiwanensis and one site of the fire-avoider Pinus morrisonicola in Taiwan. The humus microbiome was dominated by an overwhelming proportion of bacteria. As a reservoir of decomposers, humus bacteria accounted for > 70% of the litter communities and showed marked differences in composition between the two Pinus species, as determined by non-metric multidimensional scaling. Such differences were associated with the abundance of bacterial genes encoding lignin-degrading enzymes, which were highest in the P. morrisonicola stand. Additionally, the humus accumulating under this fire-avoider was characterized by low ammonium concentrations and lower pH compared with that under the fire-tolerator, which is indicative of conditions conducive to litter decomposition. Conclusively, our findings suggested that P. morrisonicola grows in more favorable conditions for needle decomposition compared with the habitats where the P. taiwanensis lives.