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Background  Dry pea production has increased substantially in North America over the last few decades. With this expansion, significant yield losses have been attributed to an escalation in Fusarium root rots in pea fields. Among the most significant rot rotting pathogenic fungal species,  Fusarium solani fsp. pisi  ( Fsp ) is one of the main causal agents of root rot of pea. High levels of partial resistance to  Fsp  has been identified in plant genetic resources. Genetic resistance offers one of the best solutions to control this root rotting fungus. A recombinant inbred population segregating for high levels of partial resistance, previously single nucleotide polymorphism (SNP) genotyped using genotyping-by-sequencing, was phenotyped for disease reaction in replicated and repeated greenhouse trials. Composite interval mapping was deployed to identify resistance-associated quantitative trait loci (QTL).    Results  Three QTL were identified using three disease reaction criteria: root disease severity, ratios of diseased vs. healthy shoot heights and dry plant weights under controlled conditions using pure cultures of  Fusarium solani fsp. pisi . One QTL  Fsp-Ps 2.1  explains 44.4–53.4% of the variance with a narrow confidence interval of 1.2 cM. The second and third QTL  Fsp-Ps3.2  and  Fsp-Ps3.3  are closely linked and explain only 3.6–4.6% of the variance. All of the alleles are contributed by the resistant parent PI 180693.    Conclusion  With the confirmation of  Fsp-Ps 2.1  now in two RIL populations, SNPs associated with this region make a good target for marker-assisted selection in pea breeding programs to obtain high levels of partial resistance to Fusarium root rot caused by  Fusarium solani fsp. pisi .    Electronic supplementary material  The online version of this article (10.1186/s12870-019-1699-9) contains supplementary material, which is available to authorized users.

Confirmation of Fusarium root rot resistance QTL Fsp-Ps 2.1 of pea under controlled conditions