The global sulfur cycle has implications for human health, climate change, biogeochemistry, and bioremediation. The organosulfur compounds that participate in this cycle not only represent a vast reservoir of sulfur, but are also used by prokaryotes as sources of energy and/or carbon. Closely linked to the inorganic sulfur cycle, it involves the interaction of prokaryotes, eukaryotes, and chemical processes. However, ecological and evolutionary studies of the conversion of organic sulfur compounds are hampered by the poor conservation of the relevant pathways and their variation even within strains of the same species. In addition, several proteins involved in the conversion of sulfonated compounds are related to proteins involved in sulfur dissimilation or turnover of other compounds. Therefore, the enzymes involved in the metabolism of organic sulfur compounds are usually not correctly annotated in public databases. To address this challenge, we have developed HMSS2, a profiled Hidden Markov Model-based tool for rapid annotation and synteny analysis of organic and inorganic sulfur cycle proteins in prokaryotic genomes. Compared to its previous version (HMS-S-S), HMSS2 includes several new features. HMM-based annotation is now supported by non-homology criteria and covers the metabolic pathways of important organosulfur compounds, including dimethylsulfpopropionate, taurine, isethionate, and sulfoquinovose. In addition, the calculation speed has been increased by a factor of four and the available output formats have been extended to include iTol compatible datasets, and customised sequence FASTA files