Transgenerational plasticity, a form of parental environmental effects, provides phenotypic variation that plays an important role in adaptation. For plants, the timing of seed germination is critical for offspring survival in stressful environments, as germination timing can alter the environmental conditions a seedling experiences. Stored seed transcripts are important determinants of seed germination, but have not previously been linked with transgenerational plasticity of germination behavior. In order for transgenerational plasticity to play an ongoing role in adaptation, there must be genetic variation for this trait segregating within species. In this study we used RNAseq and growth chamber experiments of the model legume M. trucantula to test whether parental exposure to salinity stress influences the expression of stored seed transcripts and early offspring traits. We detected genotype-dependent parental environmental effects (transgenerational plasticity) on the expression levels of stored seed transcripts, seed size, and germination behavior of four M. truncatula genotypes. Across all genotypes, more than 50% of the transcripts detected in the mature, ungerminated seed transcriptome were annotated as regulating seed germination, some of which are involved in abiotic stress response and post-embryonic development. Gentoypes TN7.22 and TN8.22, showed increased seed size in response to parental exposure to salinity stress, but no parental environmental influence on germination timing. In contrast, genotypes TN1.13 and TN1.15 showed no seed size differences across contrasting parental conditions but displayed transgenerational plasticity for germimation timing, with significantly delayed germination in saline conditions when parental plants were exposed to salinity. We conducted a coexpression network analysis and found significant sub-networks derived from salt responsive transcripts in TN1.13 and TN1.15 that are involved in post-transcriptional regulation of the germination pathway. Consistent with the delayed germination response to saline conditions in these genotypes, we found significant clustering of correlated genes associated with dormancy and up-regulation of abscisic acid (ABA). Our results demonstrate genetic variation in transgenerational plasticity within M. truncatula and show that parental exposure to salinity stress influences the expression of stored seed transcripts, seed weight, and germination behavior. Observed transgenerational plastic responses to salinity may be adaptive as soil salinity levels decrease during the germination season, but tests of adaptation requires future studies. Furthermore, we observed that parental environmental effects were due to differential seed provisioning or seed transcript expression, suggesting that different mechanisms may play a role in germination and early seedling characters in M. truncatula. We identified potential genes/transcripts that will be the focus of future studies on salinity adaptation in M. truncatula. Our coexpression analysis suggests crosstalk between stress and dormancy pathways that influence germination timing in some genotypes within natural populations. Furthermore, we show that the parental environment influences gene expression to modulate biological pathways that are likely responsible for offspring germination responses to salinity stress.