Over the past twenty years, the development of biotechnologies has led to significant evolutions in the legal protection of innovations involving plants . The scope of objects eligible for industrial property protection has noticeably expanded. In the past, in Europe at least, only plant varieties could be protected using a single instrument, the Plant Variety Certificate (COV). Since the 1990s, however, with the development of genetic engineering, a choice has been made to allow patent protection to a wide range of biotechnology inventions in addition to plant varieties. There are many reasons for this change: the influence of the American model; the belief of industrial property actors that patents can help sustain new developments in plant breeding, especially in terms of genetic engineering; and the eagerness of those involved in plant variety innovations, who invested massively in genetically modified plants in the 1980s, to protect their creations. Directive 98/44/EC of July 6, 1998 on the legal protection of biotechnological inventions supported this change and contributed to developing the sector of plant genetic engineering. Yet this directive led to greater deeper complexity in the rules that should apply to innovations, while producing socio-economic effects that were appreciated by some and criticized by others. The former consider that this major evolution in protecting innovation involving seeds answered the need to protect seeds created through biotechnology, which were not covered by the acts on plant varieties. The latter (researchers, breeders, farmers, and the general public) feared a double-edged phenomenon: an oligopolistic evolution of the seed economic sector (in 2009, the three leading seed firms accounted for more than 34% of the world seed market, all species included), and further closure. The strengthening and extension of intellectual property rights in the area of plant innovation indeed led to noticeable closing. Besides plant varieties protected by acts on plant varieties, a wide array of innovations is now protected by patents: processes, groups of plants—genetically modified or not— genes and traits, sometimes native species , and more. This change created technological lockdowns on plant genetic resources, which represent a problem because these resources are the “raw material” for innovation in breeding. This closing can also be seen in the means available to inventors and breeders in defending their intellectual property rights: some recent legislative changes facilitate judicial action (for example the law on the fight against counterfeiting, of October 29, 2007) or offer plant variety rights holders the ability to assert their rights against farmers (see Council regulation (EC) 2100/94 on Community plant variety rights, July 27, 1994 ; and the laws of August 4, 2008 and December 8, 2011), or deal with the risks of competitors gaining an economic hold on their breeding success. Beyond this, diverse contractual policies initiated by some breeders aim at giving them a more solid monopoly over their inventions as well (according to the practice of “seed-wrap” or “bag-tag” licenses). Following the Plant Biotechnology and Industrial Property Recommendation of the Committee on Economic, Ethical and Social Issues of the French High Council for Biotechnology (HCB), on June 12, 2013, this article provides an in-depth look into the relationships between industrial property and agricultural biotechnologies in the light of these changes. Firstly, the serious risks of impediment to plant innovation are noted. Truly, on the whole, the changes to acts on plant varieties do not seem to create a problem. The notion of EDVs was successfully integrated and seems to have produced beneficial effects. The development of “bag-tag” licenses aimed at preventing reverse engineering, however, deserves particular attention, because it jeopardizes the breeder’s exemption. Yet the changes to patents are the main source of concern. A series of factors could hinder breeding programmes: a proliferation of patents which are either unknown by some breeders because of a lack of information or so broad that they lead to technological lockdown. The legal scope of some of these patents is uncertain, which makes it difficult to decide whether a process or a product can be used freely. The absence of breeder’s exemption, stricto sensu, in patent law also compromises the future of breeding processes. Moreover, the many patents on plants created through biological processes or native genes and traits can constitute an additional source of blockage. This evolution in industrial property has an impact from the point of view of farmers as well. The issue of farms saving seeds remains a stumbling block between breeders and farmers. Obviously, a better balance needs to be found between these interests, and this could help maintain a sphere of autonomy for farmers. Finally, the development of new plant breeding techniques puts the farmers at risk of infringement (gene flow, the natural presence of a patented element in a crop variety). The law must take this into account.