Sedimentary and hydrothermal pyrites contained in selected Malaysian black shale and cherts have been analysed using laser ablation inductively coupled plasma (LA ICP-MS) and electron probe microanalysis (EPMA) at the University of Tasmania, Australia. This study shows that gold is concentrated in sedimentary and hydrothermal pyrite in the Middle Permian to Late Triassic black shales and Devonian cherts. According to LA ICP-MS analysis, gold contents in pyrite varied from 0.5 to 0.8 ppm Au in the Permo-Triassic black shale and between 0.2 and 0.8 ppm Au in the Devonian cherts. The lowest level of gold (0.3 ppm Au) was observed in the Permo-Triassic black shale that crops out at the Selinsing gold mine. In the Permo-Triassic period, the selenium contents display one peak (average range: 63.4–103.4 ppm Se) that is far from any gold deposit and one lowest point (average: 5.3 ppm Se) at the Selinsing gold deposit. In the Devonian period, the selenium content in sedimentary pyrite shows a peak (72.6–243.8 ppm Se) in the cherts. EPMA and LA ICP-MS data show consistent Se content variation in the Devonian and Permo-Triassic periods. Using selenium as a proxy for atmospheric oxygenation, the lowest level of Se content in the Permo-Triassic period is believed to decrease atmospheric oxygenation, as recorded in sedimentary pyrite found in black shale from the Selinsing gold deposit. The two peaks of selenium contents are interpreted as periods of increased atmospheric oxygenation. From an exploration perspective, the concentration of gold in sedimentary pyrites makes them sources for gold in the central sedimentary basin of Peninsular Malaysia. Therefore, the two maximum levels of Se and gold content during Permo-Triassic and Devonian times correspond to two stratigraphic levels of potential for orogenic gold mineralisation in the district. The EPMA data show significant values of Co over Ni in pyrite from the Gua Musang, Semantan, and Karak formation black shales, indicating a volcanic contribution of Co during the formation of sedimentary pyrite. Based on the current study’s findings, gold exploration should not be restricted to areas in and around the Selinsing gold mine, Buffalo Reef, Penjom mine, Tersang mine, and Bukit Koman mine but can be extended to BRSZ Units 1 and 2, Gua Musang, and Karak formations in the central belt of Peninsular Malaysia.