Checklists of any confined locality are very pertinent not only to academic researchers, but also to the policy makers in formulating biodiversity conservation strategies. The Tatra Mountains are the highest mountain peaks of the Carpathian Mountain range, located at the border between Slovakia and Poland, certified by UNESCO as a MAB Biosphere Reserve. More than 100 lakes of various sizes and depths are present in the valleys of this mountainous terrain, which were under severe acidification till late 1980s and recovered during 2000 after control of air pollution. For many years these lakes have witnessed several floristic and ecological studies. But, to facilitate the research, the available baseline information of algal floristics was of 25 years old. Thus, the present inventory was intented to update the existing information. It comprises of 557 cyanobacterial and algal taxa belonging to 228 genera and 95 families of the phyla Cyanobacteria, Stramenopiles, Alveolata, Cryptophyta, Chlorophyta, Charophyta and Euglenophyta. In the checklist, Forty-nine taxa (8.79%) are significantly updated to the existing records from the surveys made during 2010/12 in the present work and some recently published records.