This research puts forward an alternative methodology for the study of knowledge accumulation and innovation production in modern biotech. It presents the results of a series of thought experiments designed to measure and contrast the effects of structural differences in the performance of Mexico and Spain's modern biotech innovation systems. Borrowing concepts from neoclassical, endogenous growth, and regional systems of innovation theories and supplementing these with empirical data analysis findings, this research introduces a systems model that helps better understand how technological changes in this sector are being shaped by the interaction of multiple factors and agents, including the government. Findings suggest that Mexico's modern bio-technology system (MBTS) as modeled is, in the short term, more efficient than that modeled for Spain, especially in the creation of new marketable products and services deriving from this technology. Further analysis, however, determines that the system is deprived from this advantage in the later mid and long terms and also becomes considerably less efficient than that modeled for Spain in various other areas. When the model for Mexico's system is supplemented with specific institutional and regulatory elements -most which are present in Spain's MBTS model- its performance improves above that of its current state and beyond that of Spain in particular key areas, including market creation. The conclusions obtained in this study help both presenting modern biotech from a Systems of Innovation perspective and producing a concise list of recommendations that can serve as reference for the design of policies to assist in revamping the current MBTS operating in Mexico.