What is the most controversial issue of biology?

"Most controversial" needs some qualifiers. Among American fundamentalist Christian communities, macroevolution is contested, but creating transgenic organisms is not of any concern. In Europe on the other hand, genetically modified food is extremely controversial, wheras macroevolution is a widely accepted theory.

Nationwide in the US, embryonic stem cell research is possibly the biggest controversy. Stem cell research is extremely promising and may be the way to cure numerous human diseases. Human embryos may be the only source of pluripotent stem cells. A large demographic opposes the destruction of human embryos.

The number of people who oppose embryonic stem cell research is by most estimates much larger than the number of people who care about other issues in Biology (such as macroevolution) and the stakes in terms of public health are likely also higher than any other issue in biology.

By those reasonable standards, embryonic stem cell research is the biggest controversy in biology in the united states for now.