Identification and analysis of phytoplankton is important for understanding the environmental parameters that are influenced by the oceans, including pollution and climate change. Phytoplanktons are studied at the single cell level using conventional light-field and fluorescence microscopy, but the technique is labour intensive. Flow cytometry enables rapid and quantitative measurements of single cells and is now used as an analytical tool in phytoplankton analysis. However, it has a number of drawbacks, including high cost and portability. We describe the fabrication of a microfluidic (lab-on-a-chip) device for high-speed analysis of single phytoplankton. The device measures fluorescence (at three wavelength ranges) and the electrical impedance of single particles. The system was tested using a mixture of three algae (Isochrysis Galbana, Rhodosorus m., Synechococcus sp.) and the results compared with predictions from theory and measurements using a commercial flow cytometer (BD FACSAria). It is shown that the microfluidic flow cytometer is able to distinguish and characterise these different taxa and that impedance spectroscopy enables measurement of phytoplankton biophysical properties.