One of the foremost issues in the field of algal taxonomy is the inability to acquire, grow, and sequence new taxa. This problem is particularly true in the study of photosynthetic euglenoids where most of the distinct taxa in culture collections have been sequenced, and many other taxa of interest have been resistant to culturing, and thus, sequencing. In an effort to address this problem, we have utilized a new technique, novel to the field of taxonomy, which allows for the sequencing of nuclear genes from a very small number of cells. Through this procedure, a DNA extraction followed by a multiple displacement amplification (MDA), taxa obtained by field collection had their genomic DNA (gDNA) amplified many fold to microgram quantities. The DNA was then used as template DNA for PCR reactions, and multiple nuclear genes were amplified successfully from several different taxa. By applying this procedure, we were able to shed new light on taxa that have been historically difficult to classify, resulting in the assignment of Euglena helicoideus (C. Bernard) M. S. Benn. et Triemer and Phacus horridus (Pochm.) M. S. Benn. et Triemer to the genus Lepocinclis.