Jatropha curcas brings attention across the developing world for biodiesel production since it grows in tropical and subtropical climates with no other competing food uses. This crop is gaining popularity in Mexico for biofuel production. Currently, there are not many reports on the native varieties and their yield to estimate the feasibility of the particular genetic resource to use it as an economic crop. So in this part of work an agronomical evaluation of yield, oil content, fatty acid types and biodiesel conversion from the two native varieties of Jatropha curcas from Mexico were compared while being produced in the same agro-climatic condition. The varieties used were based on the phorbol ester content like toxic and nontoxic varieties collected from Yucatan and Veracruz. It was found that the oil content in the seeds of toxic variety was 57% and oil content of the nontoxic variety was 54% and also the seed yield is higher. The fatty acid content also varies among the two varieties like 21% and 23% in toxic and nontoxic varieties respectively. Again in the nontoxic variety the content of monosaturated fatty acid was higher, which suggests that better quality biodiesel may be expected from this genotype. Transestrification of the two kinds of oil was done using KOH as a catalyst, but no significant difference was observed in the conversion of biodiesel among the two types of oil from the two genotypes.