The rotifer Brachionus plicatilis shows a typical sigmoid growth curve, where calorie restriction (CR) and hypoxia are thought to be introduced at high population density in the stationary phase. CR may induce a shift from aerobic to anaerobic metabolism in this stationary phase, possibly contributing to an increased hypoxia tolerance. This study was undertaken to investigate the effect of CR on hypoxia tolerance at the molecular level. When rotifers were cultured under CR (fed every second day) or fed ad libitum (AL), and subsequently exposed to hypoxia, those in the CR group had a higher survival rate than their AL counterparts. We then cloned cDNAs encoding three glycolytic enzymes, glyceraldehyde 3-phosphate dehydrogenase (GAPDH), enolase (ENO), and phosphoglycerate mutase (PGM) and compared their accumulated mRNA levels between CR and AL rotifers at ages of 1–8 days by quantitative real-time PCR. The CR group showed significantly higher mRNA levels of GAPDH and ENO than their AL counterparts. Furthermore, rotifers in the stationary phase showed higher mRNA levels of these enzymes than those in the exponential growth phase. These results suggest that CR induces anaerobic metabolism, which possibly contributes to population stability under hypoxia in the stationary phase.