Six indole alkaloids with various levels of prenylation were isolated from the thermophilic fungus Talaromyces thermophilus strain YM3-4. Their structures were identified by NMR and MS spectroscopic analyses. Compounds 1 and 2 are new analogues of the key versatile precursor notoamide E. Compound 3 is a novel analogue of preechinulin, and compound 4 was reported as a natural occurring cyclo(glycyltryptophyl) for the first time. The metabolite profile of this thermophilic organism displayed a biosynthetic pathway for talathermophilins.