While telling his story, the narrator shows his audience the two white flowers – "not unlike very large white mallows" (7.6) – that Weena stuffed in his pockets. When he finishes his story, his dinner guests consider these flowers as evidence: they're weird flowers, so they could be proof that he actually did time travel. But in the Epilogue, the unnamed narrator decides to treat the flowers as symbols. He asks himself what these flowers mean, and this is the answer he comes up with:
And I have by me, for my comfort, two strange white flowers – shrivelled now, and brown and flat and brittle – to witness that even when mind and strength had gone, gratitude and a mutual tenderness still lived on in the heart of man. (Epilogue.1)
So for the narrator, the flowers are symbols of good things. He may be wrong, though, so let's ask the question he seems to be asking himself: What do these flowers represent?
Well, to begin with, let's note that these aren't the first flowers to appear in the book. When the Eloi first see the Time Traveller, they put a necklace of flowers on him, which makes the future sound kind of like Hawaii (4.6). Then they start giving him more and more flowers. Weena also gives him flowers after he saves her from drowning (5.23). So the narrator seems justified in his belief that the flowers are connected with nice things: friendship, welcome, tenderness, and beauty.
That kind of sounds like the Eloi themselves, doesn't it? The Time Traveller mentions that the flowers are "delicate," like the Eloi (4.6). But in the future, "delicate" has a downside – things that are delicate are also weak. Now, there are some differences between people and flowers – for example, flowers are purposefully bred by people, as the Time Traveller notes: "We improve our favourite plants and animals [...] gradually by selective breeding" (4.25). This is, for the Time Traveller, "the subjugation of Nature" (4.25). In other words: Humans 1, Nature 0.
People, on the other hand, are not purposefully bred toward some end. But in both cases, the end result is the same. In the future, we have flowers and people who are both delicate and beautiful, sweet but weak. With that in mind, it looks more like Nature is beating the Human team.
So there are a few things those flowers could represent: (1) the kindness that survives in the future; (2) the weakness that survives in the future; (3) the fact that people are subject to nature's laws.
For more on this, check out the use of other images of nature, like the word "garden." For instance, in 4.22, the Time Traveller calls the world a "waste garden." What does this mean?