Papaver species, well known for their alkaloids, have been used for the treatment of several diseases, such as inflammation, diarrhea, depression, and sleep disorders in certain parts of Anatolia. In this study, four Papaver species (P. lacerum, P. syriacum, P. glaucum and P. rhoeas) were collected from different localities of Turkey. Methanolic extracts were prepared from the aerial parts of the plants. A rapid analytical method was developed for the simultaneously quantitative analysis of two alkaloids, pronuciferine and roemerine, using liquid chromatography tandem mass spectrometry. Multiple reaction monitoring in the positive ionization mode was used for detection. Pronuciferine and roemerine were analyzed on a C column (2.1 × 50 mm, 3 μm) with the mobile phase run in the gradient mode with 0.1% formic acid in water (A) and 0.1% formic acid in acetonitrile at a flow rate of 0.3 mL/min. The transitions 312.1→283.1 m/z and 280.0→249.0 m/z were used to monitor pronuciferine and roemerine, respectively. The assay was linear in the concentration range of 0.01 μg/mL to 1 μg/mL (r = 0.996 for roemerine, r = 0.998 for pronuciferine). The validation studies revealed that the method was linear, sensitive, accurate, precise, selective, repeatable, robust, and rugged. Finally, the developed method was applied to quantify pronuciferine and roemerine in the selected species. The amounts of pronuciferine and roemerine were respectively found as 8.5 to 48 μg/g and 4.4 to 43,000 μg/g.