Abstract Motivation Skeletal muscles have indispensable functions and also possess prominent regenerative ability. The rapid emergence of Next Generation Sequencing (NGS) data in recent years offers us an unprecedented perspective to understand gene regulatory networks governing skeletal muscle development and regeneration. However, the data from public NGS database are often in raw data format or processed with different procedures, causing obstacles to make full use of them. Results We provide SKmDB, an integrated database of NGS information in skeletal muscle. SKmDB not only includes all NGS datasets available in the human and mouse skeletal muscle tissues and cells, but also provide preliminary data analyses including gene/isoform expression levels, gene co-expression subnetworks, as well as assembly of putative lincRNAs, typical and super enhancers and transcription factor hotspots. Users can efficiently search, browse and visualize the information with the well-designed user interface and server side. SKmDB thus will offer wet lab biologists useful information to study gene regulatory mechanisms in the field of skeletal muscle development and regeneration. Availability and implementation Freely available on the web at http://sunlab.cpy.cuhk.edu.hk/SKmDB. Supplementary information Supplementary data are available at Bioinformatics online.