The resistance to antimicrobials and biocides observed in mycobacteria which do not cause tuberculosis (MNT) determines the necessity to develop drugs. The present study evaluated the activity of naphthoquinones and heterocyclic derivatives obtained from lapachol against Mycobacterium kansasii, M. marinum, and M. abscessus, through the REMA method. It was observed that lapachol was inactive against the three mycobateria species, while β-lapachone and nor-β-lapachone showed activity only against M. marinum. The most active substances for M. kansasii were the derivates 2, 3, 7, and 11, in which compound 2 (CMI = 0.96 μM) was the most active. For M. marinum, 2, 11, and 14 were the most active, while against M. abcessus the compound 3 was the only active. The results showed a wide and diversified resistance spectrum among the species studied, which could be related to the molecular structure and position of the substituting groups, indicating the potentiality of these molecules as antimicrobial prototypes.