Abstract The strong legacy of apartheid and the consequent correlation between education and wealth have meant that, generally speaking, poorer South African students perform worse academically. Although racial segregation has been abolished for 18 years now, schools which served predominantly White students under apartheid remain functional, while those which served Black students remain dysfunctional and unable to impart the necessary numeracy and literacy skills students should be acquiring by this level. The present study provides an overview of this dualistic nature of the primary education system in South Africa, with special attention paid to the bimodality of student performance. It argues that there are in fact two different education systems in South Africa and thus two different data-generating processes. These two sub-systems can be seen when splitting student performance by former-department, language, or socioeconomic status. The implications of such a dualistic schooling system are also elucidated, with special emphasis on government reporting and econometric modeling. The recently released SACMEQ III dataset is used for the econometric modeling. The study finds that when modeling student performance separately for the wealthiest 25% of schools on the one hand, and the poorest 75% of schools on the other, there are stark differences in the factors influencing student performance. Only five of the 27 factors are shared between the two models for mathematics, and 11 of the 30 factors for reading. This suggests a bifurcated system where the process which converts inputs into outputs is fundamentally different for each sub-system. Ultimately the paper has two logical conclusions: 1) Observing averages in South African education is uniquely misleading and overestimates the educational achievement of the majority of students, and 2) Modeling a single schooling system when there are in fact two school systems can lead to spurious results and misleading policy conclusions.