The low-temperature (368 K) synthesis of silicalite-1 nanocrystals in anionic microemulsions is reported. In the presence of AOT/isooctane mixtures silicalite-1 nanocrystals can be formed that are coffin-shaped and approximately 100 x 40 x 200 nm in size. This is in contrast to samples made without the microemulsion under the same conditions where irregular spherical particles approximately 100 nm in diameter are formed. The current work shows that, in contrast to previous work in this area, the anionic microemulsions cannot stabilize colloidal silica due to the strong repulsive electrostatic forces between the anionic silicate species and the surfactant headgroup. The crystal morphology of the silicalite-1 obtained is also shown to be sensitive to the surfactant identity as syntheses using SDS/heptane/butanol mixtures lead to different morphologies. It is also possible to uncouple zeolite nucleation from growth in these systems. This was demonstrated by adding a solution containing 25 nm silicalite-1 nanocrystals to the AOT/isooctane mixture, which leads to large micron-sized spheres of silicalite-1 containing large mesopores. This report demonstrates that anionic microemulsions lead to fundamentally different crystal habits than the nonionic or cationic microemulsions investigated previously. The future outlook for the use of microemulsion-mediated zeolite growth is also discussed.