The diversity of chilis in Oaxaca is one of the most extensive in Mexico. Growers select seeds in the traditional manner; information on its quality is unknown. The aim of this research was to compare the physical and physiological quality of seeds and seedlings of three native types to chili (Huacle, De agua and Pasilla) and of the commercial Green pepper as control. Fifteen variables were evaluated in seed and twelve in seedlings. The laboratory experiments were established under a completely randomized design. Means of the variables were compared using the Tukey test (α=0.05). Results showed that Pasilla chili had the highest values in seed size and weight, which was 1.44 g heavier than the control and 2.09 to 3.73 g higher than native types. Haucle chili and green pepper had a 90% germination rate, while chili De agua and Pasilla chili had germination rates of 51 and 38%, respectively. Huacle chili had the highest germination rate index (29.89) and seedling vigor index (992.25). The top highest values of number of normal seedlings were obtained in the control and Huacle chili seedlings (72 and 88%); also, the latter had the longest plumule (3.36 cm) and radicle (7.67 cm) values. Both Huacle and Pasilla chili seedlings had larger values in height, stem thickness, number of leaves, leaf area and slenderness index than De agua and Green pepper. Huacle chili had good physical and physiological quality similar to the seeds of the commercial Green pepper.