Partners are often similar in terms of their physical and behavioural traits, such as their education, political affiliation and height. However, it is currently unclear what exactly causes this similarity—partner choice, partner influence increasing similarity over time or confounding factors such as shared environment or indirect assortment. Here, we applied Mendelian randomization to the data of 51,664 couples in the UK Biobank and investigated partner similarity in 118 traits. We found evidence of partner choice for 64 traits, 40 of which had larger phenotypic correlation than causal effect. This suggests that confounders contribute to trait similarity, among which household income, overall health rating and education accounted for 29.8, 14.1 and 11.6% of correlations between partners, respectively. Finally, mediation analysis revealed that most causal associations between different traits in the two partners are indirect. In summary, our results show the mechanisms through which indirect assortment increases the observed partner similarity.