You'll need to loop through the elements of the hash and conditionally add them to the array. Something like this (my Java is rusty, so this is just to give you an idea):

No magic here, you have to iterate on the entries:

1. HashMap<String, String> hm = new HashMap<String, String>();
2. 
   
3. hm.put("Pinus", "Tree");
4. hm.put("Juniper", "Tree");
5. hm.put("Spore", "Herb");
6. hm.put("Grass", "Weed");
7. hm.put("Algae", "Marine");
8. hm.put("Oak", "Tree");
9. hm.put("Dandelion", "Weed");
10. 
    
11. List<String> trees = new ArrayList<String>();
12. for (String k : hm.keySet())
13. {
14.   if (hm.get(k).equals("Tree"))
15.   {
16.     trees.add(k);
17.   }
18. }
19. println(trees);

After reading your question I assume that to want to reorganise the data so that you can retrieve all plants of a particular type e.g. Tree, Weed etc.

The code below extends on answer from phi.lho to do just that and if you run it you get the following output.

============================================
Plants of type Tree
  Oak
  Juniper
  Pinus
============================================
============================================
Plants of type Weed
  Grass
  Dandelion
============================================
============================================
Plants of type Carnivore
  None found:
============================================

1. import java.util.Map.Entry;
2. 
   
3. // Original HashMap with data
4. HashMap<String, String> hm = new HashMap<String, String>();
5. 
   
6. // New hashMap with ALL data reorganised using the plant
7. // type as the key. This also allows for multiple plants
8. // of a particular type by using an ArrayList as the
9. // HashMap value
10. HashMap<String, ArrayList<String>> plants = new HashMap<String, ArrayList<String>>();
11. 
    
12. // Used to hold all plants of a particular type
13. ArrayList<String> plantsOfType;
14. 
    
15. void setup()
16. {
17.   // Setup initial data in hashmap
18.   hm.put("Pinus", "Tree");
19.   hm.put("Juniper", "Tree");
20.   hm.put("Spore", "Herb");
21.   hm.put("Grass", "Weed");
22.   hm.put("Algae", "Marine");
23.   hm.put("Oak", "Tree");
24.   hm.put("Dandelion", "Weed");
25. 
    
26.   String pname, type;
27.   // Loop through all entries in the HashMap
28.   for (Entry<String, String> mapEntry : hm.entrySet()){
29.     pname = mapEntry.getKey();    // e.g. Juniper
30.     type = mapEntry.getValue();   // e.g. Tree
31.     // Attempt to get existing list for this type
32.     plantsOfType = plants.get(type);
33.     // If it does not exist create it and add to new Map
34.     if(plantsOfType == null){
35.       plantsOfType = new ArrayList<String>();
36.       plants.put(type, plantsOfType);
37.     }
38.     // Add this plant
39.     plantsOfType.add(pname);
40.   }
41.   displayByType("Tree");
42.   displayByType("Weed");
43.   displayByType("Carnivore");
44. }
45. 
    
46. // Use new HashMap to display all plants of a particular type
47. void displayByType(String type)
48. {
49.   println("============================================");
50.   println("Plants of type " + type);
51.     plantsOfType = plants.get(type);
52.     if(plantsOfType == null){
53.       println("  None found:");
54.     }
55.     else {
56.        for(String p :  plantsOfType){
57.          println("  " + p);
58.        }
59.     }
60.   println("============================================");
61. }

Thanks everyone!  This is exactly what I was looking for.