High-throughput screening of enhanced green fluorescent protein (EGFP) gene-trap transformants of filamentous fungus was achieved for the first time using an image analyzer to measure their fluorescent intensity. For quantitative analysis of EGFP fluorescent intensity per unit cell mass, we developed a method for measurement of cell mass using the fluorescent dye SP-DiI. This method offers an effective and convenient tool for screening transformants expressing fluorescent protein as a reporter, and for quantitative analysis of fungal cell mass at mug levels.