High mountain ecosystems are generally considered to be particularly sensitive to global climate change. Studies of pedogenesis associated with altitudinal variation, vegetation type and soil carbon content on the same type of parent rock are very limited in inter-tropical mountain areas. Therefore the altitudinal variation of soil pedogenesis through 9 selected profiles from the altitude of 1340 m to 3143 m asl, the summit of the Fan Si Pan Mountain, in the north of Vietnam was examined. Fan Si Pan Mountain is composed of a homogenous alkaline granite rock and is the highest point of the Inter-tropical Continental Asia. The Soil Organic Matter properties (C, N, δ13C and δ15N contents) of the different grain-size fractions of the topsoil of 4 selected profiles corresponding to different ecosystems were also examined. Three zones of different soil forming processes were present: Acrisols and Alisols at lower altitudes in sub montane forest, Podzols formed in montane and upper montane forest while Umbrisols formed at high altitude where the forest vegetation had given way to a shrubby vegetation or a steppe composed of dwarfed bamboo. With altitude, soils become sandier, have higher concentration of SiO2 and are lower in Al2O3. The selective Fe and Al oxalate (Feo and Alo) and pyrophosphate (Fep and Alp) extracts show a clear discrepancy between Acrisols or Umbrisols with no clear variation with soil depth and Podzols with high enrichment in their Bs horizon. The SOM status is highly dependent of the organic matter input by the vegetation. In Acrisols, the SOC is linked to the fine fraction within the soil profile with rapid turnover and low C/N values. Podzols are formed by the accumulation on soil surface of OM enriched in the coarse fraction with depleted δ15N and high C/N values. The organic matter input is exogenic and probably seasonal from leaves forming the surface litter while in Acrisols or Umbrisols the SOC is mainly linked to the fine fraction, and with constant δ15N values at depth. In Umbrisols, the SOC origin seems to be linked with endogenic inputs deep in the soil profile mostly produced by the decay of bamboo roots. In this tropical mountainous soil catena, the soil carbon mineralization depends not only on temperature and organo-metallic complexes that stabilize the non labile carbon pool but also is controlled by the pedogenetic process, which is linked with the vegetal ecosystem change with altitude.