A method involving flash chromatography, semi-preparative phenylhexyl RP HPLC-DAD-ELSD combined with analytic polar-RP HPLC-DAD, was applied to separate and purify six highly nitrogenated bases and a bicyclic amidine alkaloid, the major components of the marine sponge Niphates digitalis. Their structures were identified as 1,8-diazabicyclo[5.4.0]undec-7-ene (1), deoxycytidine (2), phenylalanine (3), adenosine (4), deoxyguanosine (5), adenine (6) and thymidine (7) on the basis of spectroscopic data analyses. This is the first report of these compounds in a marine sponge belonging to the Niphates genus and the first evidence of the presence of 1 from a natural source.