Abstract Background Anaerobic germination is a critical trait for rice cultivation, particularly in regions that experience flooding or waterlogging immediately after sowing. Under direct-seeded conditions, where rice is sown directly into the field without prior transplantation, the ability of seeds to germinate in anaerobic (oxygen-deficient) conditions becomes essential for successful crop establishment. This trait is especially relevant in areas prone to waterlogging, were traditional methods of rice cultivation, such as puddled transplanting, may be less viable. Understanding the genetic basis of anaerobic germination can lead to the development of rice varieties that are better adapted to such challenging conditions, thus supporting more sustainable agricultural practices. Results In this study, a nested association mapping (NAM) population consisting of 384 breeding lines was utilized to identify genomic regions associated with anaerobic germination in rice. Through comprehensive analysis, 19 significant marker-trait associations (MTAs) were identified, including 12 associations specifically linked to percent seed germination under anaerobic conditions. These associations were distributed across six different chromosomes: 3, 4, 5, 6, 7, and 9. Notably, a cluster of single nucleotide polymorphisms (SNPs) spanning a 6.9 Mb genomic region on chromosome 3 (from 21,089,181 to 28,017,712 bp) was consistently associated with percent germination at 15 and 21 days after sowing over multiple years. Similarly, a 6.4 Mb genomic segment on chromosome 6 (from 18,028,538 to 24,492,161 bp) was also associated with percent germination at the same time points. Specific SNPs within this region, namely S6_18028538 and S6_24492161, were linked to germination at 15 and 21 days, respectively. In addition to these findings, one MTA was identified for days to 50% flowering on chromosome 1, and six MTAs were identified for grain yield across chromosomes 1, 2, 5, 8, and 10. The breeding lines that exhibited both high and stable yields, along with anaerobic germination traits, have the potential to be particularly valuable in genomics-assisted breeding programs aimed at improving rice varieties for flood-prone areas. Conclusions This study provides crucial insights into the genetic basis of anaerobic germination in rice, highlighting specific genomic regions associated with this trait under direct-seeded conditions. The identification of significant MTAs across multiple chromosomes, particularly the consistent associations found on chromosomes 3 and 6, underscores the potential for developing rice varieties with enhanced tolerance to anaerobic conditions. The high-yielding breeding lines identified in this research, which also exhibit strong anaerobic germination traits, represent valuable genetic resources for breeding programs. These findings support the use of direct-seeded rice (DSR) as a sustainable alternative to traditional puddled transplanting, particularly in regions prone to flooding, thereby contributing to the development of more resilient rice cultivation practices.