The objective of this study was to evaluate the effect of anaerobic fermentation on the in vitro ruminal production of total gas (TG), methane (CH4), carbon monoxide (CO) and hydrogen sulfide (H2S), as well as on the characteristics of ruminal fermentation and CH4 conversion efficiency of whole-plant maize (WPM) from four native maize genotypes (Amarillo, Olotillo, Tampiqueño and Tuxpeño) from Mexico, and a commercial hybrid was used as a control. In all genotypes, the fermented WPM produced the lowest amounts (p ≤ 0.0236) of TG and CH4 from degraded dry matter (DM), and Tampiqueño and Tuxpeño presented the highest production of these gases. In addition, Tuxpeño also presented the highest proportion of CH4 (mL 100 mL−1 TG), and Olotillo presented the lowest proportion of both gases. Something similar occurred in H2S, where the fermented WPM produced the lowest (p ≤ 0.0077) amount per DM degraded, and Amarillo and Tampiqueño presented the highest and lowest production, respectively. However, the fermented WPM presented the highest (p = 0.0128) CO production from degraded DM, and Tuxpeño and Olotillo presented the highest and lowest production, while the rumen pH was lower (p < 0.0001) in the fermented WPM, and Tuxpeño and Olotillo presented the highest and lowest pH, respectively. Furthermore, the fermented plant presented the greatest (p ≤ 0.0055) DM degradation, and the Amarillo and hybrid genotypes presented the highest percentages, while Olotillo presented the lowest. The short-chain fatty acid (SCFA) content and metabolizable energy (ME) did not differ (p ≥ 0.0899) between genotypes and were higher (p = 0.0009) in the fresh WPM. Despite the above, the fermented WPM was more efficient (p ≤ 0.0249), and the Amarillo and hybrid genotypes produced less CH4 per unit of SCFAs, ME and organic matter. In conclusion, the Amarillo genotype equaled the hybrid one, and although the production of CO increased, anaerobic fermentation showed the potential to reduce the rumen production of TG, CH4 and H2S, as well as to improve DM degradability and CH4 conversion efficiency.