Certification within organic agriculture exhibits flexibility with respect to practices used to demonstrate that a product meets published quality standards. This case study of Mexican certified-organic agriculture finds two forms. Indigenous smallholders of southern Mexico undertake a low-input, process-oriented organic farming in which certification is based upon extensive document review, group inspections, and assessment of on-farm capacity to produce organic inputs. More recently, northern Mexican large agribusiness producers have implemented certifications based upon laboratory testing and assessment of purchased inputs. To specify these differences, this article examines large and small producers in Mexico's organic agriculture sector based on a diagnostic census of Mexican organic agriculture in 668 production zones and field surveys in 256 production zones in which 28 indicators were analyzed. After comparing the organic cultivation and certification practices of large, agro-industrial, input-oriented private firms versus small, cooperatively organized, indigenous and peasant groups, we analyze the implications of this duality for certification frameworks. We argue (with Raynolds, L., 2004. The globalization of organic agro-food networks. World Development 32(5), 725-743; Gonzalez A.A., and Nigh, R., 2005. Smallholder participation and certification of organic farm products in Mexico. Journal of Rural Studies; DeLind, L., 2000. Transforming organic agriculture into industrial organic products: reconsidering national organic standards. Human Organization 59(2), 198-208) that the increasing bureaucratic requirements of international organic certification privilege large farmers and agribusiness-style organic cultivation and present the possibility of a new entrenchment of socio-spatial inequality in Mexico. While organic and fair trade agriculture has been touted as an income-generating production strategy for small producers of the Global South, our study suggests that Mexican organic agriculture reproduces existing social inequalities between large and small producers in conventional Mexican agriculture.