Share-ploughed tillage with residue removed (CT-R) is the traditional tillage practice in the Highlands of Madagascar. No-tillage with residue mulching (NT+R) is nowadays often used as an alternative cultivation practice. Soils (0-5 cm layer) were sampled in Spring 2003 from both management systems after 11 years of soybean-maize annual rotation on a clayey Ferralsol. Soil aggregate stability can influence soil organic carbon (SOC) storage by its protection from microbial decomposition. The soil organic carbon (SOC) content was significantly impacted by systems and crop residues derived-carbon represented 64% of the annual benefit in SOC of NT+R system. The carbon associated with soil water stable macro- (200-2000 µm), meso- (20-200 µm) and microaggregates (<20 µm) from both systems, and their physical protection was studied by an incubation experiment of intact vs. crushed aggregates. Results showed macroaggregate content was significantly higher in NT+R than in CT-R system and mesoaggregate content was significantly higher in CT-R than in NT+R. Macroaggregates associated-C were 1.8 time higher in NT+R than in CT-R (31.9 and 17.9 g C g-1 soil, respectively) and made up the largest percentage (>80%) of the difference of SOC content between NT+R and CT-R systems. The amount of mineralized C over 28 days was higher in NT+R than in CT-R, and higher in meso- than in macroaggregates. However, crushing aggregates did not significantly affect the amount of mineralized C in macro- and mesoaggregates for both management systems. The macro- and mesoaggregates protected-C was lower than 54 µg g-1 soil for both NT+R and CT-R systems. Hence, the physical protection of C in aggregate larger than 50 µm was not the main process of C protection in the studied systems. Thus, C protection might occur in aggregates larger or smaller than 50 µm via physico-chemical protection mechanisms by association of organic matter to clay and silt fractions, or by protection due to chemical c