In Republic of Moldova (RM), starting from 2012, it has outlined a new accounting sector - tax on income from operational activity (TIOA), applied as a result of enactment of a new tax regime for small and medium enterprises (SMEs), by supplementing the Fiscal Code with a section related the Tax regime for economic subjects of small and medium enterprises sector. The legislative changes have led to additional questions for economic agents, although they were made in order to tax advantage the SMEs and simplify their accounting. The implementation of a new tax regime and accounting for SMEs is little researched in academic environment. In this article the author tried to come up with treatments related to some aspects of methodology of aplication the tax regime for economic agents from SMEs sector, to analyze the similar international taxation for description of TIOA accounting methodology from our country. The basic problem of this sector is the imperfect legislation, inefficient both in the field of taxation and as well as in accounting. In the process of achieving of intended purpose, the author has investigated the normative acts in force in the country and abroad, has used the methods and classic instruments of investigation.