I believe the most convenient method is 18S rDNA (using MapDraw as reference). For Chlorella I have heard that sequence analysis of nuclear rDNA internal transcribed spacer (ITS) is more appropriate, but I never performed this analysis.
The most commonly used DNA sequences are as Carlos said 18SrDNA and the ITS region, 18SrDNA is useful for green microalgae identification at the genus level but not the species because it is a conserved region. I prefer using ITS region for species identification because it is more variable and informative.