The Queretaro semi-arid region, in central Mexico, harbors one of the main threatened cacti assemblages in the Chihuahua Desert, the richest cactus diversity area in the world. For several decades, endangered cacti have been associated with a complex problem for their survival, including mainly anthropogenic disturbance and illegal collecting. Threatened species are frequently recognized as biologically rare, given their limited special distribution and abundance. Nevertheless, the influence of potential risk factors on the natural development of threatened cacti is largely unknown. Thus, a set of disturbance factors was evaluated to assess their effects on threatened populations. Fragmentation and destruction of habitat derived from human activities, as well as the lack of seedlings and the extremely low density of some species, were found to be the major causes influencing the natural development of plants and threatening the cacti community. Results suggest that partial and total habitat transformation, as well as adverse demographic features should be considered as the major risk for cacti vulnerability and survival. Conservation measures should also include protection of the dry environment, since it is a critical and key element and could decrease the extinction risk of this cacti assemblage.