Quinoa (Chenopodium quinoa Willd.) is an annual protein-rich pseudocereal native to the Andean region of South America. Quinoa has been recognized as a potentially important crop in terms of global food and nutrition security since it can thrive in harsh environments and has an excellent nutritional profile. Our collaborative group and two other independent groups have sequenced the quinoa genome. Subsequently, we also have developed more than 150 genotyped quinoa inbred lines suitable for molecular analyses. One of the limiting factors in quinoa research had been lacking molecular breeding techniques such as genetic transformation. Here, we show that apple latent spherical virus (ALSV) can be used for two virus-mediated transient expression techniques, virus-induced gene silencing (VIGS) and virus-mediated overexpression (VOX) in quinoa to promote the functional genomics studies. Our data show that the ALSV vector can be used in a broad range of quinoa inbred lines derived from the northern and southern highland and lowland sub-populations. We also report a progress on functional analyses of flowering regulators in quinoa using the virus vector systems. Quinoa is a short-day plant by its origin but shows varying day-length response between the genotypes. Quinoa can flower under varying photoperiods although flowering mechanisms and associated regulators in quinoa have been unrevealed yet. We found that VOX or VIGS of quinoa flowering-gene homologs modulated flowering time in quinoa. The usefulness of the virus vector system in quinoa for evaluating gene function will be discussed.