Organotin compounds are causing deterioration effect on non-targeted aquatic species in the environment, such as shell anomalies in oysters and imposex in gastropods, even at concentrations as low nanograms per litre. Specific analytical methods have been developed for different environmental matrices. Analysis of organotin compounds in sediment because of hydrophobic properties and tend to adsorb onto particulate matter is valuable for assessing the environmental distribution and fate. Therefore, in this study, a rapid, reliable, sensitive and effective method developed for quantification and identification of antifouling organotin butyl- and phenyltin compounds in sediment samples by using Gas chromatography with Tandem MS detector (GC-MSMS and GC-QTOF). The method is based on the single extraction step followed by GC-MSMS and GC-QTOF detection. The sample extraction steps were decreased for low labour laboratory costs and time-consuming. Not only the extraction procedure but instrumental method parameters were carefully optimised in order to increase sensitivity and precision. The QTOF system with the help of mass accuracy and mass resolution showed a good sensitivity and precision to analyse sediment samples. The isotopic disturbance and utilisation isotopic space for confirmation of organotin compounds have been scrutinised in GC-QTOF. GC Triple Quadrupole (GC-MSMS) system also utilised as a secondary confirmation method for organotin compound analysis. Additionally, the sensitivity of both MS detectors under the matrix effect was investigated. The recoveries of extraction were in the range of 82-106%. The acquired results have shown that the concentration range in 10-250 ppb (ng/ml) level was denoted good linearity (r(2) = 0.9725-0.9983). Moreover, limits of detection (LOD) for both butyl and phenyl fractions of organotin compounds were ranged between 0.23 and 22.11 pg/ml. Consequently, the developed method successfully was applied to certificated reference material (BCR - 462) and the targeted organotin compounds in a real marine/harbour sediment sample.