Plants can produce a variety of secondary metabolites that may be associated with the species or genus to which they belong, as well as numerous other factors, such as circadian rhythm, plant development stage, seasonality, soil, etc. Nectandra megapotamica belong to the genus Nectandra rol. Ex rottb. and on literature few chemical studies are demonstrated. To evaluate the variability of apolar and polar compounds of N. megapotamica and its histolocalization, different tests were conducted. For analysis of apolar metabolites, the leaves of 11 individuals of N. megapotamica were dried, ground and the essential oil extracted by hydrodistillation method and injected on GC-MS. The mass signals obtained from raw data files were extracted and aligned within the metAlign software program, regrouped using the MSClust software and analyzed in Metaboanalyst 3.0 platform using principal component analysis (PCA) and biplot of loadings and samples of N. megapotamica. For histological analysis, the leaves were cut by hand; the adaxial abaxial was scraped, the volatile compounds extracted by SPME and evaluated by GC-MS. For analysis of the polar compounds, the leaves were sprayed, the extract prepared in ethanol/water, analyzed by LC-DAD-MS/MS and the identification was based on the mass spectra obtained by ESI, retention time, UV/VIS (λmax) and fragmentation in the negative mode. Fifty-two apolar compounds were identified by GC-MS, among them phenylpropanoids (from 0 to 52.7%), hydrocarbons monoterpenes (from 0 to 19.8%), hydrocarbons sesquiterpenes (from 2.8 to 92.3%) and oxygenated sesquiterpenes (from 0 to 94, 5%). The analysis of PCA and biplot revealed the presence of two groups, with the punctual influence of isoespatulenol, α-bisabolol, bicyclogermacreno and elemicin on the separation between the samples. The five samples collected on the state of São Paulo presented a particular pattern, where all the samples were collected simultaneous places and they presented high variations of terpenes, especially α-bisabolol, with a range from 1.6% to 93.7%. Analysis of the polar metabolism of these samples by LC-DAD-MS/MS demonstrated a highly similar pattern among the compounds present in these samples, with the identification of proanthocyanidins and flavonoids O and C glycosides. Histochemical analyses suggested the location of the essential oils on idioblasts and analyzes by CG-MS revealed no difference in the location of the volatiles in the abaxial or adaxial faces, even between of individuals that have apolar compounds variability. In summary, were found individuals of the same species that produce different apolar compounds have unchanged polar compounds and the terpenes localization.