Integration of crop and livestock production systems constitutes an important engine for agricultural development and enhancement of smallholder farmers’ livelihoods in the least developed countries. For the last forty years, the Malian cotton sub-sector has recorded mixed growth trends, having been initially successful before declining and then catching up. The growth dynamics in the cotton subsector has permitted smallholder farmers to endow and improve their living condition. The purpose of this study was to establish smallholder farmers’ dynamics of integrating crop and livestock production systems as well as classification of the systems and their trajectories. The study was carried out in different agro-ecological zones in Southern Mali. A multistage sampling technique was used to select the area of study. Stratified random sampling technique was then used to select 134 smallholder farming households from three villages. A panel datasets was used from the Malian Company of Textile Development (CMDT) from 1961 to 2014 and 1974 to 2014. Based on explanatory structure variables, principal component analysis (PCA) and ascending hierarchical classification (AHC) were used to distinguish smallholder farmers’ dynamics as well as classify them into different classes or groups. Five types of smallholder were distinguished. Type 1 was super large families representing 14% of the total smallholder farmers. Type 2 consists of large families, and constituted of 28% of the smallholder farmers. Type 3 consists of medium-sized families which represented 28% of the total smallholder farmers. Type 4 and type 5 were small and young families with 19 and 11% of smallholder farmers respectively. Notably, small family farming was low in Southern Mali, and so some agricultural options can be developed such as the milk and meat value chains among others.