The forecast for the first quarter of this century is that the issue of teaching science in the language to which the learner is most familiar will receive more attention in our quest to win more students for science. Over two-thirds of countries in Africa, Asia, and Europe have developed policies on the use of the mother tongue for teaching science in the lower levels of their education system. In spite of this policy thrust, the educational system of many of these countries has not responded fully to the demands of such a policy. Because studies which mapped the dynamics of communication in science classrooms taught using the mother tongue are scant, we remain in the dark as to how best to structure such classrooms. The study was conducted in 12 primary schools and it involved 36 teachers in urban and rural locations of Lagos State, Nigeria. Quantitative and qualitative data were collected from primary science classrooms where the mother tongue is expected to be used as a medium of instruction. Mismatch between policy and practice was found especially in urban science classrooms. Among other things, it was found that on the average, science lessons delivered in primary 1 in rural settings, were found to be 93.6% in the mother tongue (L1). In primary 2 this fell to 91.1% and in primary 3–84.6%. In contrast, in the urban schools, mother tongue content was found to be 61.8% in primary 1, 49.2% in primary 2 and 26.6% in primary 3. The geo-spatial communication between and among pupils in urban and rural science classes also showed interesting findings, that is, English served as a mediating language. The implications of the findings for future policy considerations and future research to inform policy are drawn.