Transequatorial F region plasma bubbles are large-scale ionospheric depleted regions that develop in the bottomside of equatorial F region due to plasma instability processes. Simultaneous all-sky imaging observations of the OI 630.0 nm and OI 777.4 nm nightglow emissions were carried out at São José dos Campos (23.21°S, 45.86°W; dip latitude 17.6°S), Brazil, during the years 2000 and 2001, a period of high solar activity. In this work we present and discuss the height-resolved nocturnal F region zonal drift velocities obtained from plasma bubbles observed in imaging observations of these two emissions for several days of 2000 and 2001. It should be pointed out that the two emissions result from different excitation mechanisms (OI 630.0 nm by dissociative recombination of O2+ and OI 777.4 nm by radiative recombination of O+) and come from different F region heights, separated by ∼50–80 km. We have investigated the nighttime zonal plasma drift variations using fixed emission peak altitudes, used by earlier investigators, as well as emission peak altitudes based on simultaneous ionospheric sounding observations. The average maximum and minimum zonal plasma drift velocities inferred for both the emissions, using emission peak altitudes based on simultaneous ionospheric observations, (OI 630.0 nm: 172 ± 2 and 89 ± 15 m/s; OI 777.4 nm: 184 ± 12 and 103 ± 16 m/s) are lower and with less scatter than those using fixed emission peak altitudes (OI 630.0 nm: 185 ± 10 and 104 ± 18 m/s; OI 777.4 nm: 202 ± 19 and 121 ± 20 m/s). Also, the nocturnal variations of the zonal plasma drift velocities obtained for the two emissions with peak altitudes based on simultaneous ionospheric observations show better agreement than for the case with fixed emission peak altitudes (h = 380 km for OI 777.4 nm and h = 300 km for OI 630.0 nm).