In this paper, RNA and DNA contents and RNA/DNA ratios obtained with two fluorometric methods for the extraction and quantification of nucleic acids in individual estuarine gobiid larvae are compared. A total of 141 gobiid larvae, collected in the Mira and Guadiana estuaries (Portugal), were analysed. This study indicated that the nucleic acids content and RNA/DNA ratios of individual larvae varied with the procedure used. The two methods yielded similar log DNA values but different log RNA and log (RNA/DNA). The differences could be due to a number of factors related to specific steps of tested protocols. Comparison of nucleic acids contents and calibration of the two methods by regression analysis provided a reasonable basis for comparison although differences between estimates were evident.