Seagrass meadowsare important carbon sinks that play a key role in the mitigation of global climate change.Proper quantification of this carbon compartment is a prerequisite to the implementation of policy initiatives related to blue carbon; however, certain aspects of carbon science and measurement practices still need to be formalized and standardized. Variation and inconsistency in assessment methods may potentially overestimate or underestimateblue carbon measurements in seagrass ecosystems.There are still gaps in knowledge and the need for scientific data on carbon sequestration from a range of geographical locations. In this paper we discuss the issue of blue carbon estimation in seagrass meadows based on a review of current literature, and identify main problems and perspectives,particularly with relevance to Indonesia. We also present results from our ongoing study to estimate blue carbon storage in several field sites representing the variation found in coastal areas of Java. Blue carbon inventory for Javaisa pertinent issue becausethe island’s seagrass and mangrove ecosystems continue to be degraded and threatened by anthropogenic activity,while the ecosystem services they providebecome increasingly more important. In this st