We have characterized micro-droplet generation using water immiscible hexafluorophosphate ([PF6])- and bis(trifluoromethylsulfonyl)imide ([Tf2N])-based room temperature ionic liquids (RTILs). The interfacial tension between total 7 RTILs and phosphate buffered saline (PBS) was measured using a tensiometer for the first time. PBS is one of the most commonly used buffer solutions in cell-related researches. The measured interfacial tension ranges from 8.51 to 11.62 and from 9.56 to 13.19 for [Tf2N]- and [PF6]-based RTILs, respectively. The RTILs micro-droplets were generated in a microfluidic device. The micro-droplet size and generation frequency were determined based on continuous monitoring of light transmittance at the interface in microchannel. The size of RTIL micro-droplets was inversely proportional to the increase of PBS solution flow rate and RTILs hydrophobicity, while droplet generation frequency was proportional to those changes. The measured size of RTILs droplets ranged from 0.6 to 10.5 nl, and from 1.0 to 17.1 nl for [Tf2N]- and [PF6]-based RTILs, respectively. The measured frequency of generated RTILs droplets ranged from 2.3 to 37.2 droplet/min, and from 2.7 to 17.1 droplet/min for [Tf2N]- and [PF6]-based RTILs, respectively. The capillary numbers were calculated depending on the RTILs, and ranged from 0.51×10.3 to 1.06×10.3 and from 5.00×10.3 to 8.65×10.3, for [Tf2N]- and [PF6]-based RTILs, respectively. The interfacial tension between RTILs and PBS will contribute to developing bioprocesses using immiscible RTILs. Also, the RTILs micro-droplets will enable the high-throughput monitoring of various biological and chemical reactions using RTILs as new reaction media.