Reports of the last decade show that some types of food and spices included in the human diet, such as pepper (Capsicum annuum L.) can have a positive effect on human health. The Mexican pepper germplasm is poorly documented with regard to variety and the amount of phytochemical compounds that it contains. In the present study, the variation of phytochemical compounds was evaluated in nine fruit variants (morphotypes) of wild and cultivated pepper grown in Oaxaca. ANOVA detected significant differences among pepper morphotypes and ripeness stages of fruits; vitamin C, total phenols, flavonoids, P-carotene, coordinated chromatic of color, and capsaicinoids. The highest values of vitamin C were found in &rsquo;Tabaquero&rsquo;, &rsquo;Guero&rsquo; and &rsquo;Costeño&rsquo; morphotypes (151.6 to 183.2 mg 100 g-1). With regard to total phenols and flavonoids, &rsquo;Piquín&rsquo; and &rsquo;Solterito&rsquo; had the highest levels. Coordinates of color a* and b*, and chroma presented a positive correlation with phenol and flavonoid contents. The evaluated morphotypes differed in capsaicin and dihydrocapsaicin; C. annuum had higher capsaicin content (4.9 to 142 /<g mL¹) than dihydrocapsaicin (1.5 to 65.5 /<g mL¹) and C. pubescens Ruiz &amp; Pav. showed the opposite pattern.