In order to enforce the concepts of bioeconomy and the circular economy, the use of a bottom-up approach at the national level has been proposed: to start at the level of a small region, encourage its development, considering its specific capacities and resources, rather than applying generalized assumptions at a national or international level. Therefore, this study has been carried out with an aim to develop a methodology for the assessment of small rural areas in the context of the circular economy and bioeconomy, in order to advance the development of these regions in an effective way, using the existing bioresources comprehensively. The methodology is based on the identification of existing and potential bioeconomy flows (land and its use, bioresources, human resources, employment and business), the identification of the strengths of their interaction and compare these with the situation at the regional and national levels in order to identify the specific region's current situation in the bioeconomy and identify more forward-looking directions for development. Several methods are integrated and interlinked in the methodology – indicator analysis, correlation and regression analysis, and heat map tables. The methodology is approbated on one case study – Aizkraukle region – a small rural region in Latvia. During the research recommendations for the development of the circular economy and bioeconomy for the case study have been elaborated.