Mangrove ecosystem has an important role in reducing carbon in the environment. There has been massive conversion of mangrove area into ponds and buildings in the current period. Therefore, the species diversity and carbon sequestration capacity of the mangrove ecosystem must be evaluated to monitor its function. This research aims to evaluate the species diversity and the sequestered carbon in the mangrove ecosystem of Karimunjawa National Park (KNP), Indonesia. The species analysis in the 3 research sites, 9 transects, and 27 plots (10 m × 10 m) that was obtained using the quadrat sampling method. Allometric equations, Shannon–Wiener, and evenness indices were used to estimate the standing biomass and carbon, species diversity, and distribution, respectively. The sediment samples were obtained at a depth of 100 cm and divided into three depths, namely, 0–33, 34–67, and 68–100 cm. The carbon content of mangrove sediments was analyzed in the laboratory using the Walkley–Black method. The results revealed that mangroves in the KNP have moderate diversity and even distribution. The estimated carbon in the mangrove stand was 146.22 t C ha–1 and the estimated carbon stock in the sediment was around 360.61 t C ha–1. Although the mangrove ecosystem in Karimunjawa National Park is still in a stable condition, it is necessary to monitor its changes due to the anthropogenic activities.