The UV–vis absorbance spectra, molar extinction coefficients and circular dichroism spectra, as well as NMR and high resolution tandem mass spectrometry spectra were determined for two prominent secondary metabolites from cyanobacteria, namely anabaenopeptin A and anabaenopeptin B. The compounds were extracted from the cyanobacterium Planktothrix rubescens CBT929 and purified by flash chromatography and HPLC. Exact amounts of isolated compounds were assessed by quantitative ¹H-NMR with internal calibrant ethyl 4-(dimethylamino)benzoate in DMSO‑d₆ at 298 K with a recycle delay (d1) of 120 s. UV–vis absorbance spectra were recorded in methanol at room temperature. Molar extinction coefficients were determined at 278 nm as 4190 M⁻¹ cm⁻¹ and 2300 M⁻¹ cm⁻¹ in methanol for anabaenopeptin A and anabaenopeptin B, respectively. Circular dichroism spectra and secondary fragmentation mass spectra are also reported.