A rapid and sensitive analytical method based on reverse-phase high-performance liquid chromatography was first developed to simultaneously determine elsinochrome C (EC) and hypocrellin A (HA) in the submerged fermentation. The mobile phase consisted of acetonitrile-water 60:40 (v/v) with a flow-rate of 1 mL/min. The calibration curves were as follows: y = 37,625x + 249,775 for EC, y = 30,813x + 556,409 for HA and linear at the investigated concentration. The correlation coefficients (R(2) ) were 0.9989 and 0.9998 respectively for EC and HA. The limits of detection and quantification were 175 and 585 µg/L for EC and 205 and 610 µg/L for HA. The precisions of concentration and retention times were less than 2.5 and 0.3%. The recovery of the method was greater than 95.0%. The methodology was applied to analyze simultaneously EC and HA concentrations in a submerged fermentation, and was adequate for analysis of biosynthesis of perylenequinones. The method was also amplified to separate and purify EC and HA using a semi-preparative C(18) column. In addition, elsinochrome C was first identified in the submerged fermentation broth of Shiraia sp. SUPER-H168.