Peroxisomal malate dehydrogenase (PMDH) oxidises NADH produced by fatty acid beta-oxidation during seed germination and seedling growth. Arabidopsis thaliana beta-oxidation mutants exhibit seed dormancy or impaired seed germination and failure of seedlings to degrade triacylglycerol (TAG), but the pmdh1 pmdh2 null mutant germinates readily and degrades TAG slowly during seedling growth. We reasoned that in the pmdh1 pmdh2 mutant an alternative means of oxidising NADH operates to allow a slow rate of beta-oxidation, such as NADH and NAD(+) transport across the peroxisomal membrane or activity of another peroxisomal oxido-reductase. Here we show that peroxisomal hydroxypyruvate reductase (HPR) is present in germinating seeds and although knocking out HPR has little effect on germination and early seedling growth, when knocked out in combination with PMDH it exacerbates the pmdh1 pmdh2 phenotype. It greatly increases the proportion of dormant seeds and reduces the rate of seed germination. Seedlings have increased sucrose dependence and resistance to 2,4-dichlorophenoxybutyric acid (2,4-DB), and slower rate of TAG breakdown. When PMDH is absent, malate is lower in amount in germinating seeds and when HPR is also absent, serine (the immediate precursor of hydroxypyruvate) is much higher. These results indicate that HPR can oxidise NADH at sufficient rate in the absence of PMDH to support beta-oxidation and hence seed germination. We conclude that while HPR normally plays little role in seed germination our results support the growing body of evidence that peroxisomal NADH cannot be exported to the cytosol for oxidation but is oxidised by resident oxido-reductases.